Starting phenix.real_space_refine on Sat Aug 8 22:35:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mu2_48617/08_2026/9mu2_48617.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mu2_48617/08_2026/9mu2_48617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2026/9mu2_48617.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2026/9mu2_48617.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2026/9mu2_48617.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mu2_48617/08_2026/9mu2_48617.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.013 sd= 0.139 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 121 5.16 5 C 19681 2.51 5 N 5207 2.21 5 O 6355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31396 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "B" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "D" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "E" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "F" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "J" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "K" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "M" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 306 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "N" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "O" Number of atoms: 299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 299 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "P" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 904 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "Q" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 324 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "R" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "S" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "T" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "U" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "V" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "W" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "X" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "Y" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "Z" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "a" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "b" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "c" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "d" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "e" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "f" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "g" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "h" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "i" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "j" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "k" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "l" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 780 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "m" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 832 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "n" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1037 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 120} Chain: "o" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1288 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain: "p" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 6.12, per 1000 atoms: 0.19 Number of scatterers: 31396 At special positions: 0 Unit cell: (115.71, 118.37, 190.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 121 16.00 P 32 15.00 O 6355 8.00 N 5207 7.00 C 19681 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.20 Conformation dependent library (CDL) restraints added in 1.2 seconds 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7188 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 22 sheets defined 32.8% alpha, 26.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 3 through 11 removed outlier: 4.323A pdb=" N VAL A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 37 removed outlier: 3.665A pdb=" N GLU A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 48 through 63 removed outlier: 4.262A pdb=" N ILE A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 97 removed outlier: 4.127A pdb=" N ALA A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 removed outlier: 4.022A pdb=" N VAL B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG B 10 " --> pdb=" O ASP B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 37 removed outlier: 3.692A pdb=" N GLU B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 48 through 63 removed outlier: 4.132A pdb=" N ILE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS B 53 " --> pdb=" O SER B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 97 removed outlier: 4.174A pdb=" N ALA B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ILE B 91 " --> pdb=" O GLU B 87 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 16 Processing helix chain 'D' and resid 70 through 86 removed outlier: 3.622A pdb=" N HIS D 74 " --> pdb=" O ASP D 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 8 No H-bonds generated for 'chain 'E' and resid 6 through 8' Processing helix chain 'E' and resid 71 through 83 removed outlier: 3.743A pdb=" N VAL E 81 " --> pdb=" O GLU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'F' and resid 165 through 169 Processing helix chain 'G' and resid 3 through 11 removed outlier: 4.324A pdb=" N VAL G 7 " --> pdb=" O THR G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 37 removed outlier: 3.658A pdb=" N GLU G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 48 through 63 removed outlier: 4.210A pdb=" N ILE G 52 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS G 53 " --> pdb=" O SER G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 97 removed outlier: 4.145A pdb=" N ALA G 90 " --> pdb=" O LYS G 86 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 11 removed outlier: 4.040A pdb=" N VAL H 7 " --> pdb=" O THR H 3 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG H 10 " --> pdb=" O ASP H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 37 removed outlier: 3.685A pdb=" N GLU H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 48 through 63 removed outlier: 4.135A pdb=" N ILE H 52 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS H 53 " --> pdb=" O SER H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 97 removed outlier: 4.203A pdb=" N ALA H 90 " --> pdb=" O LYS H 86 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 17 through 19 No H-bonds generated for 'chain 'J' and resid 17 through 19' Processing helix chain 'J' and resid 70 through 86 removed outlier: 3.650A pdb=" N HIS J 74 " --> pdb=" O ASP J 70 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 8 No H-bonds generated for 'chain 'K' and resid 6 through 8' Processing helix chain 'K' and resid 71 through 83 removed outlier: 3.700A pdb=" N VAL K 81 " --> pdb=" O GLU K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 152 Processing helix chain 'L' and resid 165 through 169 Processing helix chain 'M' and resid 14 through 37 removed outlier: 3.744A pdb=" N GLN M 37 " --> pdb=" O ARG M 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 37 removed outlier: 4.433A pdb=" N PHE N 17 " --> pdb=" O SER N 13 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG N 30 " --> pdb=" O LYS N 26 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N PHE N 31 " --> pdb=" O SER N 27 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS N 32 " --> pdb=" O VAL N 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 37 removed outlier: 3.983A pdb=" N PHE O 17 " --> pdb=" O SER O 13 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG O 19 " --> pdb=" O ALA O 15 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP O 36 " --> pdb=" O LYS O 32 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN O 37 " --> pdb=" O ARG O 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 8 through 47 removed outlier: 4.117A pdb=" N GLN P 12 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N ASP P 21 " --> pdb=" O LYS P 17 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP P 22 " --> pdb=" O THR P 18 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG P 44 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 56 through 58 No H-bonds generated for 'chain 'P' and resid 56 through 58' Processing helix chain 'P' and resid 78 through 85 Processing helix chain 'P' and resid 95 through 113 removed outlier: 3.700A pdb=" N VAL P 101 " --> pdb=" O PRO P 97 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS P 104 " --> pdb=" O GLU P 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.301A pdb=" N VAL S 7 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 37 removed outlier: 3.668A pdb=" N GLU S 24 " --> pdb=" O GLU S 20 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 47 No H-bonds generated for 'chain 'S' and resid 45 through 47' Processing helix chain 'S' and resid 48 through 63 removed outlier: 4.206A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LYS S 53 " --> pdb=" O SER S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 97 removed outlier: 4.133A pdb=" N ALA S 90 " --> pdb=" O LYS S 86 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ILE S 91 " --> pdb=" O GLU S 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.039A pdb=" N VAL T 7 " --> pdb=" O THR T 3 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG T 10 " --> pdb=" O ASP T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 18 through 37 removed outlier: 3.709A pdb=" N GLU T 24 " --> pdb=" O GLU T 20 " (cutoff:3.500A) Processing helix chain 'T' and resid 45 through 47 No H-bonds generated for 'chain 'T' and resid 45 through 47' Processing helix chain 'T' and resid 48 through 63 removed outlier: 4.135A pdb=" N ILE T 52 " --> pdb=" O PHE T 48 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS T 53 " --> pdb=" O SER T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 97 removed outlier: 4.172A pdb=" N ALA T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE T 91 " --> pdb=" O GLU T 87 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN T 94 " --> pdb=" O ALA T 90 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 16 Processing helix chain 'V' and resid 70 through 85 removed outlier: 3.661A pdb=" N HIS V 74 " --> pdb=" O ASP V 70 " (cutoff:3.500A) Processing helix chain 'W' and resid 6 through 8 No H-bonds generated for 'chain 'W' and resid 6 through 8' Processing helix chain 'W' and resid 71 through 83 removed outlier: 3.687A pdb=" N VAL W 81 " --> pdb=" O GLU W 77 " (cutoff:3.500A) Processing helix chain 'W' and resid 147 through 152 Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'Y' and resid 3 through 11 removed outlier: 4.330A pdb=" N VAL Y 7 " --> pdb=" O THR Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 37 removed outlier: 3.669A pdb=" N GLU Y 24 " --> pdb=" O GLU Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 47 No H-bonds generated for 'chain 'Y' and resid 45 through 47' Processing helix chain 'Y' and resid 48 through 63 removed outlier: 4.200A pdb=" N ILE Y 52 " --> pdb=" O PHE Y 48 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS Y 53 " --> pdb=" O SER Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 85 through 97 removed outlier: 4.019A pdb=" N ALA Y 90 " --> pdb=" O LYS Y 86 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE Y 91 " --> pdb=" O GLU Y 87 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 11 removed outlier: 4.062A pdb=" N VAL Z 7 " --> pdb=" O THR Z 3 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG Z 10 " --> pdb=" O ASP Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 18 through 37 removed outlier: 3.683A pdb=" N GLU Z 24 " --> pdb=" O GLU Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 45 through 47 No H-bonds generated for 'chain 'Z' and resid 45 through 47' Processing helix chain 'Z' and resid 48 through 63 removed outlier: 4.119A pdb=" N ILE Z 52 " --> pdb=" O PHE Z 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 97 removed outlier: 4.085A pdb=" N ALA Z 90 " --> pdb=" O LYS Z 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE Z 91 " --> pdb=" O GLU Z 87 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 16 Processing helix chain 'b' and resid 17 through 19 No H-bonds generated for 'chain 'b' and resid 17 through 19' Processing helix chain 'b' and resid 70 through 86 removed outlier: 3.641A pdb=" N HIS b 74 " --> pdb=" O ASP b 70 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 8 No H-bonds generated for 'chain 'c' and resid 6 through 8' Processing helix chain 'c' and resid 71 through 83 removed outlier: 3.678A pdb=" N VAL c 81 " --> pdb=" O GLU c 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 147 through 152 Processing helix chain 'd' and resid 165 through 169 Processing helix chain 'e' and resid 3 through 11 removed outlier: 4.355A pdb=" N VAL e 7 " --> pdb=" O THR e 3 " (cutoff:3.500A) Processing helix chain 'e' and resid 18 through 37 removed outlier: 3.654A pdb=" N GLU e 24 " --> pdb=" O GLU e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 45 through 47 No H-bonds generated for 'chain 'e' and resid 45 through 47' Processing helix chain 'e' and resid 48 through 63 removed outlier: 4.197A pdb=" N ILE e 52 " --> pdb=" O PHE e 48 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS e 53 " --> pdb=" O SER e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 97 removed outlier: 4.067A pdb=" N ALA e 90 " --> pdb=" O LYS e 86 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE e 91 " --> pdb=" O GLU e 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 11 removed outlier: 4.027A pdb=" N VAL f 7 " --> pdb=" O THR f 3 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG f 10 " --> pdb=" O ASP f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 37 removed outlier: 3.701A pdb=" N GLU f 24 " --> pdb=" O GLU f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 47 No H-bonds generated for 'chain 'f' and resid 45 through 47' Processing helix chain 'f' and resid 48 through 63 removed outlier: 4.146A pdb=" N ILE f 52 " --> pdb=" O PHE f 48 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS f 53 " --> pdb=" O SER f 49 " (cutoff:3.500A) Processing helix chain 'f' and resid 85 through 97 removed outlier: 4.122A pdb=" N ALA f 90 " --> pdb=" O LYS f 86 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ILE f 91 " --> pdb=" O GLU f 87 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN f 94 " --> pdb=" O ALA f 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 16 Processing helix chain 'h' and resid 70 through 86 removed outlier: 3.507A pdb=" N HIS h 74 " --> pdb=" O ASP h 70 " (cutoff:3.500A) Processing helix chain 'i' and resid 6 through 8 No H-bonds generated for 'chain 'i' and resid 6 through 8' Processing helix chain 'i' and resid 71 through 83 removed outlier: 3.727A pdb=" N VAL i 81 " --> pdb=" O GLU i 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 147 through 152 Processing helix chain 'j' and resid 165 through 169 Processing helix chain 'k' and resid 3 through 11 removed outlier: 4.310A pdb=" N VAL k 7 " --> pdb=" O THR k 3 " (cutoff:3.500A) Processing helix chain 'k' and resid 18 through 37 removed outlier: 3.634A pdb=" N GLU k 24 " --> pdb=" O GLU k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 47 No H-bonds generated for 'chain 'k' and resid 45 through 47' Processing helix chain 'k' and resid 48 through 63 removed outlier: 4.228A pdb=" N ILE k 52 " --> pdb=" O PHE k 48 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS k 53 " --> pdb=" O SER k 49 " (cutoff:3.500A) Processing helix chain 'k' and resid 85 through 97 removed outlier: 4.068A pdb=" N ALA k 90 " --> pdb=" O LYS k 86 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE k 91 " --> pdb=" O GLU k 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 removed outlier: 4.053A pdb=" N VAL l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG l 10 " --> pdb=" O ASP l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 18 through 37 removed outlier: 3.690A pdb=" N GLU l 24 " --> pdb=" O GLU l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 45 through 47 No H-bonds generated for 'chain 'l' and resid 45 through 47' Processing helix chain 'l' and resid 48 through 63 removed outlier: 4.172A pdb=" N ILE l 52 " --> pdb=" O PHE l 48 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS l 53 " --> pdb=" O SER l 49 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 97 removed outlier: 4.135A pdb=" N ALA l 90 " --> pdb=" O LYS l 86 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE l 91 " --> pdb=" O GLU l 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 16 Processing helix chain 'n' and resid 17 through 19 No H-bonds generated for 'chain 'n' and resid 17 through 19' Processing helix chain 'n' and resid 70 through 86 removed outlier: 3.597A pdb=" N HIS n 74 " --> pdb=" O ASP n 70 " (cutoff:3.500A) Processing helix chain 'o' and resid 6 through 8 No H-bonds generated for 'chain 'o' and resid 6 through 8' Processing helix chain 'o' and resid 71 through 83 removed outlier: 3.731A pdb=" N VAL o 81 " --> pdb=" O GLU o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 147 through 152 Processing helix chain 'p' and resid 165 through 169 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 73 removed outlier: 5.934A pdb=" N THR A 69 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N THR B 69 " --> pdb=" O TYR B 80 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR k 69 " --> pdb=" O TYR k 80 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER k 77 " --> pdb=" O GLU l 71 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLU l 71 " --> pdb=" O SER k 77 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA k 79 " --> pdb=" O THR l 69 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N THR l 69 " --> pdb=" O TYR l 80 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR e 69 " --> pdb=" O TYR e 80 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER f 70 " --> pdb=" O ALA e 79 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N THR f 69 " --> pdb=" O TYR f 80 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N THR Y 69 " --> pdb=" O TYR Y 80 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER Y 77 " --> pdb=" O GLU Z 71 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU Z 71 " --> pdb=" O SER Y 77 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA Y 79 " --> pdb=" O THR Z 69 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N THR Z 69 " --> pdb=" O TYR Z 80 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR S 69 " --> pdb=" O TYR S 80 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N SER S 77 " --> pdb=" O GLU T 71 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N GLU T 71 " --> pdb=" O SER S 77 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA S 79 " --> pdb=" O THR T 69 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR T 69 " --> pdb=" O TYR T 80 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR G 69 " --> pdb=" O TYR G 80 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N THR H 69 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.386A pdb=" N ILE C 82 " --> pdb=" O GLU C 97 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLU C 97 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LYS C 63 " --> pdb=" O PRO C 35 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 44 through 48 Processing sheet with id=AA4, first strand: chain 'D' and resid 22 through 23 removed outlier: 4.239A pdb=" N VAL D 61 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASN D 59 " --> pdb=" O PRO D 42 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N SER D 44 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP D 57 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG D 46 " --> pdb=" O SER D 55 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N SER D 55 " --> pdb=" O ARG D 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 67 current: chain 'D' and resid 95 through 108 removed outlier: 6.800A pdb=" N SER D 123 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N THR D 101 " --> pdb=" O THR D 121 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N THR D 121 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE D 103 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER D 119 " --> pdb=" O ILE D 103 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN D 105 " --> pdb=" O HIS D 117 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N HIS D 117 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL D 107 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LEU D 115 " --> pdb=" O VAL D 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 115 through 127 current: chain 'J' and resid 36 through 48 removed outlier: 4.229A pdb=" N VAL J 61 " --> pdb=" O LYS J 40 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASN J 59 " --> pdb=" O PRO J 42 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER J 44 " --> pdb=" O ASP J 57 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP J 57 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ARG J 46 " --> pdb=" O SER J 55 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER J 55 " --> pdb=" O ARG J 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 54 through 67 current: chain 'J' and resid 95 through 108 removed outlier: 6.819A pdb=" N SER J 123 " --> pdb=" O ASP J 99 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR J 101 " --> pdb=" O THR J 121 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N THR J 121 " --> pdb=" O THR J 101 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ILE J 103 " --> pdb=" O SER J 119 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER J 119 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLN J 105 " --> pdb=" O HIS J 117 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N HIS J 117 " --> pdb=" O GLN J 105 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL J 107 " --> pdb=" O LEU J 115 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU J 115 " --> pdb=" O VAL J 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 115 through 127 current: chain 'V' and resid 36 through 48 removed outlier: 4.220A pdb=" N VAL V 61 " --> pdb=" O LYS V 40 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASN V 59 " --> pdb=" O PRO V 42 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER V 44 " --> pdb=" O ASP V 57 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP V 57 " --> pdb=" O SER V 44 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG V 46 " --> pdb=" O SER V 55 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N SER V 55 " --> pdb=" O ARG V 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 54 through 67 current: chain 'V' and resid 95 through 108 removed outlier: 6.547A pdb=" N SER V 123 " --> pdb=" O ASP V 99 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR V 101 " --> pdb=" O THR V 121 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR V 121 " --> pdb=" O THR V 101 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE V 103 " --> pdb=" O SER V 119 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER V 119 " --> pdb=" O ILE V 103 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLN V 105 " --> pdb=" O HIS V 117 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS V 117 " --> pdb=" O GLN V 105 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL V 107 " --> pdb=" O LEU V 115 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU V 115 " --> pdb=" O VAL V 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 115 through 127 current: chain 'b' and resid 36 through 48 removed outlier: 4.109A pdb=" N VAL b 61 " --> pdb=" O LYS b 40 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ASN b 59 " --> pdb=" O PRO b 42 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER b 44 " --> pdb=" O ASP b 57 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASP b 57 " --> pdb=" O SER b 44 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG b 46 " --> pdb=" O SER b 55 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER b 55 " --> pdb=" O ARG b 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 54 through 67 current: chain 'b' and resid 95 through 108 removed outlier: 5.636A pdb=" N PHE b 96 " --> pdb=" O PHE b 127 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N PHE b 127 " --> pdb=" O PHE b 96 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLU b 98 " --> pdb=" O LYS b 125 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N LYS b 125 " --> pdb=" O GLU b 98 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP b 100 " --> pdb=" O SER b 123 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'b' and resid 115 through 127 current: chain 'h' and resid 36 through 48 removed outlier: 4.252A pdb=" N VAL h 61 " --> pdb=" O LYS h 40 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN h 59 " --> pdb=" O PRO h 42 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER h 44 " --> pdb=" O ASP h 57 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP h 57 " --> pdb=" O SER h 44 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ARG h 46 " --> pdb=" O SER h 55 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N SER h 55 " --> pdb=" O ARG h 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 54 through 67 current: chain 'h' and resid 95 through 108 removed outlier: 6.788A pdb=" N SER h 123 " --> pdb=" O ASP h 99 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N THR h 101 " --> pdb=" O THR h 121 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR h 121 " --> pdb=" O THR h 101 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE h 103 " --> pdb=" O SER h 119 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER h 119 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLN h 105 " --> pdb=" O HIS h 117 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N HIS h 117 " --> pdb=" O GLN h 105 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL h 107 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU h 115 " --> pdb=" O VAL h 107 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'h' and resid 115 through 127 current: chain 'n' and resid 36 through 48 removed outlier: 5.516A pdb=" N PHE n 37 " --> pdb=" O TRP n 65 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N TRP n 65 " --> pdb=" O PHE n 37 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ILE n 39 " --> pdb=" O ASP n 63 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ASP n 63 " --> pdb=" O ILE n 39 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N MET n 41 " --> pdb=" O VAL n 61 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL n 61 " --> pdb=" O MET n 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'n' and resid 54 through 67 current: chain 'n' and resid 95 through 108 removed outlier: 6.843A pdb=" N SER n 123 " --> pdb=" O ASP n 99 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR n 101 " --> pdb=" O THR n 121 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR n 121 " --> pdb=" O THR n 101 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE n 103 " --> pdb=" O SER n 119 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N SER n 119 " --> pdb=" O ILE n 103 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLN n 105 " --> pdb=" O HIS n 117 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N HIS n 117 " --> pdb=" O GLN n 105 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N VAL n 107 " --> pdb=" O LEU n 115 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU n 115 " --> pdb=" O VAL n 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 24 through 25 current: chain 'E' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 56 through 65 current: chain 'E' and resid 105 through 122 removed outlier: 6.015A pdb=" N GLU E 132 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE E 117 " --> pdb=" O GLU E 130 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU E 130 " --> pdb=" O PHE E 117 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N LEU E 119 " --> pdb=" O GLU E 128 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU E 128 " --> pdb=" O LEU E 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 128 through 135 current: chain 'K' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 24 through 25 current: chain 'K' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 56 through 65 current: chain 'K' and resid 105 through 122 removed outlier: 6.033A pdb=" N GLU K 132 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE K 117 " --> pdb=" O GLU K 130 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU K 130 " --> pdb=" O PHE K 117 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU K 119 " --> pdb=" O GLU K 128 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N GLU K 128 " --> pdb=" O LEU K 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 128 through 135 current: chain 'W' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 24 through 25 current: chain 'W' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 56 through 65 current: chain 'W' and resid 105 through 122 removed outlier: 6.001A pdb=" N GLU W 132 " --> pdb=" O ASN W 115 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHE W 117 " --> pdb=" O GLU W 130 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLU W 130 " --> pdb=" O PHE W 117 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU W 119 " --> pdb=" O GLU W 128 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N GLU W 128 " --> pdb=" O LEU W 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 128 through 135 current: chain 'c' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 24 through 25 current: chain 'c' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 56 through 65 current: chain 'c' and resid 105 through 122 removed outlier: 6.021A pdb=" N GLU c 132 " --> pdb=" O ASN c 115 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N PHE c 117 " --> pdb=" O GLU c 130 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU c 130 " --> pdb=" O PHE c 117 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU c 119 " --> pdb=" O GLU c 128 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLU c 128 " --> pdb=" O LEU c 119 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 128 through 135 current: chain 'i' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 24 through 25 current: chain 'i' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 56 through 65 current: chain 'i' and resid 105 through 122 removed outlier: 5.827A pdb=" N HIS i 114 " --> pdb=" O GLY i 134 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N GLY i 134 " --> pdb=" O HIS i 114 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'i' and resid 128 through 135 current: chain 'o' and resid 24 through 25 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 24 through 25 current: chain 'o' and resid 56 through 65 WARNING: can't find start of bonding for strands! previous: chain 'o' and resid 56 through 65 current: chain 'o' and resid 105 through 122 removed outlier: 6.030A pdb=" N GLU o 132 " --> pdb=" O ASN o 115 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N PHE o 117 " --> pdb=" O GLU o 130 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLU o 130 " --> pdb=" O PHE o 117 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU o 119 " --> pdb=" O GLU o 128 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLU o 128 " --> pdb=" O LEU o 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 41 through 43 removed outlier: 3.577A pdb=" N ASP E 41 " --> pdb=" O THR E 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 27 through 30 removed outlier: 5.412A pdb=" N ILE I 82 " --> pdb=" O GLU I 97 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLU I 97 " --> pdb=" O ILE I 82 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS I 63 " --> pdb=" O PRO I 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 44 through 48 Processing sheet with id=AA9, first strand: chain 'K' and resid 42 through 43 Processing sheet with id=AB1, first strand: chain 'O' and resid 2 through 8 removed outlier: 3.546A pdb=" N ILE M 6 " --> pdb=" O SER P 74 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'U' and resid 5 through 13 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 27 through 30 current: chain 'U' and resid 57 through 63 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 57 through 63 current: chain 'U' and resid 78 through 87 removed outlier: 5.390A pdb=" N ILE U 82 " --> pdb=" O GLU U 97 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU U 97 " --> pdb=" O ILE U 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 44 through 48 Processing sheet with id=AB4, first strand: chain 'W' and resid 41 through 43 removed outlier: 3.555A pdb=" N ASP W 41 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 27 through 30 removed outlier: 5.405A pdb=" N ILE a 82 " --> pdb=" O GLU a 97 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLU a 97 " --> pdb=" O ILE a 82 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS a 63 " --> pdb=" O PRO a 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 44 through 48 Processing sheet with id=AB7, first strand: chain 'c' and resid 41 through 43 removed outlier: 3.512A pdb=" N ASP c 41 " --> pdb=" O THR c 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'g' and resid 27 through 30 removed outlier: 5.394A pdb=" N ILE g 82 " --> pdb=" O GLU g 97 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU g 97 " --> pdb=" O ILE g 82 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYS g 63 " --> pdb=" O PRO g 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'g' and resid 44 through 48 Processing sheet with id=AC1, first strand: chain 'i' and resid 41 through 43 removed outlier: 3.525A pdb=" N ASP i 41 " --> pdb=" O THR i 52 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'm' and resid 27 through 30 removed outlier: 5.381A pdb=" N ILE m 82 " --> pdb=" O GLU m 97 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU m 97 " --> pdb=" O ILE m 82 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N LYS m 63 " --> pdb=" O PRO m 35 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'm' and resid 44 through 48 Processing sheet with id=AC4, first strand: chain 'o' and resid 41 through 43 removed outlier: 3.562A pdb=" N ASP o 41 " --> pdb=" O THR o 52 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.31 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9154 1.33 - 1.45: 5092 1.45 - 1.57: 17483 1.57 - 1.69: 62 1.69 - 1.81: 218 Bond restraints: 32009 Sorted by residual: bond pdb=" C1' DT R 20 " pdb=" N1 DT R 20 " ideal model delta sigma weight residual 1.468 1.516 -0.048 1.40e-02 5.10e+03 1.19e+01 bond pdb=" C3' DG R 17 " pdb=" C2' DG R 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.23e+00 bond pdb=" C3' DA Q 1 " pdb=" C2' DA Q 1 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.78e+00 bond pdb=" C3' DT Q 16 " pdb=" C2' DT Q 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.40e+00 bond pdb=" C3' DT Q 2 " pdb=" O3' DT Q 2 " ideal model delta sigma weight residual 1.435 1.400 0.035 1.30e-02 5.92e+03 7.09e+00 ... (remaining 32004 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 41631 2.17 - 4.35: 1520 4.35 - 6.52: 112 6.52 - 8.70: 0 8.70 - 10.87: 1 Bond angle restraints: 43264 Sorted by residual: angle pdb=" O4' DA R 7 " pdb=" C1' DA R 7 " pdb=" N9 DA R 7 " ideal model delta sigma weight residual 108.00 111.31 -3.31 7.00e-01 2.04e+00 2.24e+01 angle pdb=" C4' DG Q 3 " pdb=" O4' DG Q 3 " pdb=" C1' DG Q 3 " ideal model delta sigma weight residual 110.10 105.69 4.41 1.00e+00 1.00e+00 1.95e+01 angle pdb=" N3 DT Q 8 " pdb=" C4 DT Q 8 " pdb=" O4 DT Q 8 " ideal model delta sigma weight residual 119.90 122.23 -2.33 6.00e-01 2.78e+00 1.51e+01 angle pdb=" N3 DT R 10 " pdb=" C4 DT R 10 " pdb=" O4 DT R 10 " ideal model delta sigma weight residual 119.90 122.23 -2.33 6.00e-01 2.78e+00 1.51e+01 angle pdb=" N3 DT Q 15 " pdb=" C4 DT Q 15 " pdb=" O4 DT Q 15 " ideal model delta sigma weight residual 119.90 122.22 -2.32 6.00e-01 2.78e+00 1.49e+01 ... (remaining 43259 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 17559 17.29 - 34.58: 1446 34.58 - 51.87: 270 51.87 - 69.15: 94 69.15 - 86.44: 53 Dihedral angle restraints: 19422 sinusoidal: 8269 harmonic: 11153 Sorted by residual: dihedral pdb=" CA ILE b 62 " pdb=" C ILE b 62 " pdb=" N ASP b 63 " pdb=" CA ASP b 63 " ideal model delta harmonic sigma weight residual -180.00 -150.64 -29.36 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE J 62 " pdb=" C ILE J 62 " pdb=" N ASP J 63 " pdb=" CA ASP J 63 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA ILE D 62 " pdb=" C ILE D 62 " pdb=" N ASP D 63 " pdb=" CA ASP D 63 " ideal model delta harmonic sigma weight residual 180.00 -151.75 -28.25 0 5.00e+00 4.00e-02 3.19e+01 ... (remaining 19419 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4203 0.094 - 0.188: 496 0.188 - 0.283: 2 0.283 - 0.377: 0 0.377 - 0.471: 1 Chirality restraints: 4702 Sorted by residual: chirality pdb=" P DA Q 1 " pdb=" OP1 DA Q 1 " pdb=" OP2 DA Q 1 " pdb=" O5' DA Q 1 " both_signs ideal model delta sigma weight residual True 2.34 2.81 -0.47 2.00e-01 2.50e+01 5.54e+00 chirality pdb=" CA PHE O 31 " pdb=" N PHE O 31 " pdb=" C PHE O 31 " pdb=" CB PHE O 31 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PHE l 85 " pdb=" N PHE l 85 " pdb=" C PHE l 85 " pdb=" CB PHE l 85 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 4699 not shown) Planarity restraints: 5530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP h 65 " -0.001 2.00e-02 2.50e+03 2.32e-02 1.35e+01 pdb=" CG TRP h 65 " -0.007 2.00e-02 2.50e+03 pdb=" CD1 TRP h 65 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP h 65 " -0.014 2.00e-02 2.50e+03 pdb=" NE1 TRP h 65 " 0.056 2.00e-02 2.50e+03 pdb=" CE2 TRP h 65 " -0.018 2.00e-02 2.50e+03 pdb=" CE3 TRP h 65 " 0.021 2.00e-02 2.50e+03 pdb=" CZ2 TRP h 65 " -0.027 2.00e-02 2.50e+03 pdb=" CZ3 TRP h 65 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP h 65 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG P 44 " -0.325 9.50e-02 1.11e+02 1.46e-01 1.32e+01 pdb=" NE ARG P 44 " 0.022 2.00e-02 2.50e+03 pdb=" CZ ARG P 44 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG P 44 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG P 44 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 30 " -0.320 9.50e-02 1.11e+02 1.44e-01 1.26e+01 pdb=" NE ARG O 30 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG O 30 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG O 30 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG O 30 " -0.011 2.00e-02 2.50e+03 ... (remaining 5527 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1737 2.72 - 3.26: 31220 3.26 - 3.81: 48503 3.81 - 4.35: 64342 4.35 - 4.90: 109304 Nonbonded interactions: 255106 Sorted by model distance: nonbonded pdb=" OD1 ASP W 74 " pdb=" NH2 ARG c 141 " model vdw 2.175 3.120 nonbonded pdb=" OD1 ASP c 74 " pdb=" NH2 ARG i 141 " model vdw 2.198 3.120 nonbonded pdb=" OH TYR J 18 " pdb=" OD2 ASP J 84 " model vdw 2.253 3.040 nonbonded pdb=" O ASP c 127 " pdb=" OD1 ASP c 127 " model vdw 2.277 3.040 nonbonded pdb=" O ASP i 127 " pdb=" OD1 ASP i 127 " model vdw 2.292 3.040 ... (remaining 255101 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'S' selection = chain 'T' selection = chain 'Y' selection = chain 'Z' selection = chain 'e' selection = chain 'f' selection = chain 'k' selection = chain 'l' } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'U' selection = chain 'a' selection = chain 'g' selection = chain 'm' } ncs_group { reference = chain 'D' selection = chain 'J' selection = chain 'V' selection = chain 'b' selection = chain 'h' selection = chain 'n' } ncs_group { reference = chain 'E' selection = chain 'K' selection = chain 'W' selection = chain 'c' selection = chain 'i' selection = chain 'o' } ncs_group { reference = chain 'F' selection = chain 'L' selection = chain 'X' selection = chain 'd' selection = chain 'j' selection = chain 'p' } ncs_group { reference = (chain 'M' and resid 1 through 37) selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.920 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 32009 Z= 0.336 Angle : 0.901 10.872 43264 Z= 0.550 Chirality : 0.057 0.471 4702 Planarity : 0.011 0.146 5530 Dihedral : 14.351 86.443 12234 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.05 % Favored : 96.92 % Rotamer: Outliers : 0.15 % Allowed : 1.95 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.13), residues: 3699 helix: -1.37 (0.13), residues: 1057 sheet: 0.14 (0.15), residues: 1212 loop : -0.25 (0.16), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG o 10 TYR 0.039 0.005 TYR P 51 PHE 0.031 0.003 PHE O 31 TRP 0.056 0.007 TRP h 65 HIS 0.009 0.002 HIS b 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.34 (32009) covalent geometry : angle 0.90127 / 0.55 (43264) hydrogen bonds : bond 0.13781 / 8.92 ( 1146) hydrogen bonds : angle 7.56671 / 5.29 ( 3192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 1555 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 11 ILE cc_start: 0.9487 (pt) cc_final: 0.9213 (mt) REVERT: B 19 ASP cc_start: 0.7873 (m-30) cc_final: 0.7611 (m-30) REVERT: B 25 ILE cc_start: 0.9091 (mt) cc_final: 0.8794 (mt) REVERT: B 29 CYS cc_start: 0.8621 (m) cc_final: 0.8171 (m) REVERT: B 68 MET cc_start: 0.8993 (mtp) cc_final: 0.8787 (mtm) REVERT: B 85 PHE cc_start: 0.8657 (m-80) cc_final: 0.8371 (m-80) REVERT: C 52 ASP cc_start: 0.8761 (m-30) cc_final: 0.8384 (m-30) REVERT: C 56 ASP cc_start: 0.8558 (t0) cc_final: 0.8049 (t0) REVERT: C 58 SER cc_start: 0.9042 (t) cc_final: 0.8667 (m) REVERT: C 86 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7172 (mtp-110) REVERT: C 98 GLU cc_start: 0.8577 (tt0) cc_final: 0.8131 (tt0) REVERT: D 119 SER cc_start: 0.9170 (t) cc_final: 0.8822 (p) REVERT: E 27 LEU cc_start: 0.8843 (mt) cc_final: 0.8641 (tp) REVERT: E 46 MET cc_start: 0.2855 (ttt) cc_final: 0.2457 (tpp) REVERT: E 56 VAL cc_start: 0.9333 (t) cc_final: 0.9073 (p) REVERT: E 93 SER cc_start: 0.8898 (t) cc_final: 0.8624 (p) REVERT: G 4 LEU cc_start: 0.8751 (tp) cc_final: 0.8172 (tp) REVERT: G 94 ASN cc_start: 0.9179 (t0) cc_final: 0.8968 (t0) REVERT: H 15 ASP cc_start: 0.7451 (p0) cc_final: 0.7100 (p0) REVERT: H 19 ASP cc_start: 0.8207 (m-30) cc_final: 0.7702 (m-30) REVERT: H 63 ILE cc_start: 0.8587 (tt) cc_final: 0.8256 (tt) REVERT: H 69 THR cc_start: 0.9196 (m) cc_final: 0.8912 (t) REVERT: H 95 TYR cc_start: 0.8241 (t80) cc_final: 0.7643 (t80) REVERT: J 15 LEU cc_start: 0.9414 (mt) cc_final: 0.9075 (mt) REVERT: J 92 ASN cc_start: 0.8428 (m110) cc_final: 0.8063 (t0) REVERT: J 109 ASP cc_start: 0.8003 (p0) cc_final: 0.7791 (p0) REVERT: K 50 TYR cc_start: 0.5205 (p90) cc_final: 0.4915 (p90) REVERT: K 90 GLU cc_start: 0.7730 (tt0) cc_final: 0.7444 (tt0) REVERT: K 91 VAL cc_start: 0.9157 (t) cc_final: 0.8954 (m) REVERT: K 126 ILE cc_start: 0.8830 (mt) cc_final: 0.8182 (mp) REVERT: O 32 LYS cc_start: 0.6974 (tttt) cc_final: 0.6749 (tttt) REVERT: P 12 GLN cc_start: 0.6472 (tt0) cc_final: 0.6034 (tp40) REVERT: P 16 MET cc_start: 0.8616 (mtp) cc_final: 0.8347 (mtp) REVERT: P 68 LEU cc_start: 0.8273 (mt) cc_final: 0.8056 (mp) REVERT: P 75 HIS cc_start: 0.7543 (m-70) cc_final: 0.7073 (m-70) REVERT: P 99 TYR cc_start: 0.7869 (t80) cc_final: 0.7382 (t80) REVERT: P 102 ILE cc_start: 0.9021 (mm) cc_final: 0.8791 (tp) REVERT: S 21 GLN cc_start: 0.7827 (mt0) cc_final: 0.7499 (mt0) REVERT: S 77 SER cc_start: 0.9104 (m) cc_final: 0.8821 (p) REVERT: S 94 ASN cc_start: 0.9470 (t0) cc_final: 0.9192 (t0) REVERT: T 19 ASP cc_start: 0.8160 (m-30) cc_final: 0.7895 (m-30) REVERT: T 23 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7730 (mt-10) REVERT: T 63 ILE cc_start: 0.8612 (tt) cc_final: 0.8378 (tp) REVERT: T 77 SER cc_start: 0.8999 (m) cc_final: 0.8601 (t) REVERT: U 8 ILE cc_start: 0.8911 (mt) cc_final: 0.8423 (tt) REVERT: U 57 VAL cc_start: 0.9269 (t) cc_final: 0.8985 (m) REVERT: V 49 TYR cc_start: 0.9056 (t80) cc_final: 0.8826 (t80) REVERT: V 79 LYS cc_start: 0.8635 (tptp) cc_final: 0.8197 (tttm) REVERT: W 46 MET cc_start: 0.0904 (ttt) cc_final: 0.0671 (tpp) REVERT: W 151 THR cc_start: 0.5541 (p) cc_final: 0.5213 (m) REVERT: Y 19 ASP cc_start: 0.8557 (m-30) cc_final: 0.8116 (m-30) REVERT: Y 20 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8024 (tp30) REVERT: Z 94 ASN cc_start: 0.8667 (t0) cc_final: 0.8347 (t0) REVERT: a 56 ASP cc_start: 0.8917 (t0) cc_final: 0.8496 (t0) REVERT: a 94 TYR cc_start: 0.8892 (m-80) cc_final: 0.8530 (m-10) REVERT: a 98 GLU cc_start: 0.8767 (tt0) cc_final: 0.8192 (tt0) REVERT: b 57 ASP cc_start: 0.8413 (t70) cc_final: 0.7932 (t0) REVERT: b 80 ARG cc_start: 0.8222 (ttt180) cc_final: 0.7811 (ttt90) REVERT: b 94 TYR cc_start: 0.9200 (m-80) cc_final: 0.8991 (m-80) REVERT: b 125 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7961 (mtpt) REVERT: c 116 LYS cc_start: 0.8910 (ttmt) cc_final: 0.8202 (ttmm) REVERT: c 129 TYR cc_start: 0.9224 (p90) cc_final: 0.8527 (p90) REVERT: e 19 ASP cc_start: 0.7964 (m-30) cc_final: 0.7731 (m-30) REVERT: e 20 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8510 (mm-30) REVERT: e 36 MET cc_start: 0.8777 (mtp) cc_final: 0.8478 (mtp) REVERT: e 51 MET cc_start: 0.9019 (mtt) cc_final: 0.8796 (ttm) REVERT: e 68 MET cc_start: 0.8429 (mtp) cc_final: 0.7939 (mtm) REVERT: f 23 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8313 (tp30) REVERT: g 49 GLU cc_start: 0.7843 (tt0) cc_final: 0.7179 (tt0) REVERT: h 32 ILE cc_start: 0.9241 (mm) cc_final: 0.8966 (mm) REVERT: h 40 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8658 (mtpp) REVERT: h 45 ASN cc_start: 0.8588 (m110) cc_final: 0.8264 (m-40) REVERT: h 69 ASP cc_start: 0.8246 (t0) cc_final: 0.7726 (t0) REVERT: h 99 ASP cc_start: 0.8012 (t0) cc_final: 0.7633 (t0) REVERT: h 116 LEU cc_start: 0.9236 (mt) cc_final: 0.8827 (mt) REVERT: i 74 ASP cc_start: 0.7360 (t0) cc_final: 0.7140 (t0) REVERT: i 102 SER cc_start: 0.9132 (m) cc_final: 0.8857 (p) REVERT: j 168 ASP cc_start: 0.8018 (t0) cc_final: 0.7813 (t70) REVERT: l 33 LEU cc_start: 0.9276 (tp) cc_final: 0.9020 (tp) REVERT: l 68 MET cc_start: 0.9007 (mtp) cc_final: 0.8316 (mtm) REVERT: l 69 THR cc_start: 0.9391 (m) cc_final: 0.9140 (p) REVERT: l 70 SER cc_start: 0.9488 (t) cc_final: 0.9255 (t) REVERT: l 74 ASP cc_start: 0.8697 (m-30) cc_final: 0.8485 (m-30) REVERT: l 78 ASN cc_start: 0.8401 (m-40) cc_final: 0.8023 (m-40) REVERT: m 8 ILE cc_start: 0.9172 (mt) cc_final: 0.8849 (tt) REVERT: n 41 MET cc_start: 0.8169 (tpt) cc_final: 0.7945 (tpp) REVERT: n 85 LEU cc_start: 0.9257 (mt) cc_final: 0.9026 (mt) REVERT: n 99 ASP cc_start: 0.8196 (t0) cc_final: 0.7994 (t0) REVERT: n 116 LEU cc_start: 0.9324 (mt) cc_final: 0.9029 (mm) REVERT: n 119 SER cc_start: 0.9419 (t) cc_final: 0.9025 (p) REVERT: o 39 ASP cc_start: 0.8202 (t0) cc_final: 0.7909 (p0) REVERT: o 40 THR cc_start: 0.8216 (p) cc_final: 0.7937 (t) REVERT: o 71 ASP cc_start: 0.7843 (p0) cc_final: 0.7544 (m-30) outliers start: 5 outliers final: 0 residues processed: 1557 average time/residue: 0.2140 time to fit residues: 511.7497 Evaluate side-chains 958 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 958 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 6.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 ASN D 30 GLN D 45 ASN D 74 HIS E 136 ASN G 32 GLN H 21 GLN J 74 HIS J 113 GLN P 14 HIS P 29 GLN V 74 HIS V 113 GLN W 124 ASN a 13 GLN a 55 ASN a 76 ASN b 74 HIS c 136 ASN f 21 GLN h 74 HIS h 113 GLN i 136 ASN k 18 GLN k 32 GLN l 21 GLN l 43 GLN m 37 ASN m 76 ASN n 74 HIS n 105 GLN n 113 GLN o 136 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.098557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081147 restraints weight = 59874.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.083793 restraints weight = 28637.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.085510 restraints weight = 16967.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086649 restraints weight = 11673.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.087430 restraints weight = 8990.021| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32009 Z= 0.160 Angle : 0.690 8.795 43264 Z= 0.383 Chirality : 0.045 0.189 4702 Planarity : 0.004 0.048 5530 Dihedral : 10.967 80.724 4537 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.49 % Allowed : 14.97 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.14), residues: 3699 helix: 0.55 (0.16), residues: 1053 sheet: 0.24 (0.15), residues: 1146 loop : 0.09 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG Z 47 TYR 0.030 0.002 TYR i 32 PHE 0.020 0.002 PHE O 17 TRP 0.022 0.002 TRP P 96 HIS 0.011 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (32009) covalent geometry : angle 0.69038 / 0.38 (43264) hydrogen bonds : bond 0.05289 / 3.41 ( 1146) hydrogen bonds : angle 5.22007 / 3.65 ( 3192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1197 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 1113 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.8373 (m-30) cc_final: 0.8119 (m-30) REVERT: B 25 ILE cc_start: 0.9178 (mt) cc_final: 0.8902 (mt) REVERT: B 85 PHE cc_start: 0.8589 (m-80) cc_final: 0.8249 (m-80) REVERT: C 52 ASP cc_start: 0.8619 (m-30) cc_final: 0.8417 (m-30) REVERT: C 58 SER cc_start: 0.9076 (t) cc_final: 0.8781 (m) REVERT: C 86 ARG cc_start: 0.8015 (ttm170) cc_final: 0.7572 (mtp-110) REVERT: D 62 ILE cc_start: 0.9160 (pt) cc_final: 0.8570 (pt) REVERT: D 88 SER cc_start: 0.9106 (t) cc_final: 0.8693 (t) REVERT: D 97 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7215 (mm-30) REVERT: D 119 SER cc_start: 0.9061 (t) cc_final: 0.8711 (p) REVERT: E 46 MET cc_start: 0.2453 (ttt) cc_final: 0.2138 (tpp) REVERT: E 84 VAL cc_start: 0.8817 (t) cc_final: 0.8597 (p) REVERT: F 168 ASP cc_start: 0.9056 (t0) cc_final: 0.8832 (t70) REVERT: G 23 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6971 (mm-30) REVERT: G 94 ASN cc_start: 0.9017 (t0) cc_final: 0.8664 (t0) REVERT: H 77 SER cc_start: 0.9258 (t) cc_final: 0.8736 (m) REVERT: H 95 TYR cc_start: 0.7964 (t80) cc_final: 0.7447 (t80) REVERT: I 13 GLN cc_start: 0.7895 (tt0) cc_final: 0.7486 (mt0) REVERT: I 32 ASP cc_start: 0.8247 (m-30) cc_final: 0.7983 (m-30) REVERT: J 1 MET cc_start: 0.7545 (mtm) cc_final: 0.7329 (mtt) REVERT: J 24 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.8281 (m) REVERT: J 27 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7306 (mm-30) REVERT: K 9 ASP cc_start: 0.7236 (m-30) cc_final: 0.6936 (m-30) REVERT: M 5 LYS cc_start: 0.9058 (mttt) cc_final: 0.8622 (mttp) REVERT: N 16 LYS cc_start: 0.8326 (tppt) cc_final: 0.7515 (tppt) REVERT: N 20 GLN cc_start: 0.8678 (mm-40) cc_final: 0.8037 (mm-40) REVERT: O 11 GLU cc_start: 0.6144 (pm20) cc_final: 0.5851 (pm20) REVERT: P 45 GLU cc_start: 0.7878 (tt0) cc_final: 0.7242 (tt0) REVERT: P 81 PHE cc_start: 0.7830 (m-80) cc_final: 0.7428 (m-10) REVERT: P 87 ARG cc_start: 0.7732 (mtp85) cc_final: 0.6466 (mmt180) REVERT: S 21 GLN cc_start: 0.7648 (mt0) cc_final: 0.7422 (mt0) REVERT: S 49 SER cc_start: 0.8806 (p) cc_final: 0.8526 (m) REVERT: S 77 SER cc_start: 0.9197 (m) cc_final: 0.8881 (p) REVERT: S 86 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8875 (mmmt) REVERT: S 94 ASN cc_start: 0.9290 (t0) cc_final: 0.9049 (t0) REVERT: T 63 ILE cc_start: 0.8506 (tt) cc_final: 0.8263 (tp) REVERT: T 77 SER cc_start: 0.8995 (m) cc_final: 0.8529 (t) REVERT: T 94 ASN cc_start: 0.8699 (t0) cc_final: 0.8229 (t0) REVERT: U 8 ILE cc_start: 0.9103 (mt) cc_final: 0.8594 (tt) REVERT: V 79 LYS cc_start: 0.8782 (tptp) cc_final: 0.8293 (tttm) REVERT: W 66 MET cc_start: 0.8681 (mtp) cc_final: 0.8466 (mtp) REVERT: W 151 THR cc_start: 0.5680 (p) cc_final: 0.5188 (m) REVERT: Y 41 VAL cc_start: 0.8077 (t) cc_final: 0.7856 (m) REVERT: Y 51 MET cc_start: 0.8841 (mtt) cc_final: 0.8609 (mtp) REVERT: Z 94 ASN cc_start: 0.8391 (t0) cc_final: 0.8100 (t0) REVERT: a 13 GLN cc_start: 0.6981 (tt0) cc_final: 0.6746 (mt0) REVERT: a 56 ASP cc_start: 0.8678 (t0) cc_final: 0.8311 (t0) REVERT: a 94 TYR cc_start: 0.8962 (m-80) cc_final: 0.8678 (m-10) REVERT: b 62 ILE cc_start: 0.9435 (mp) cc_final: 0.9146 (mt) REVERT: c 129 TYR cc_start: 0.9138 (p90) cc_final: 0.8440 (p90) REVERT: e 68 MET cc_start: 0.8103 (mtp) cc_final: 0.7788 (mtm) REVERT: f 74 ASP cc_start: 0.9152 (m-30) cc_final: 0.8861 (m-30) REVERT: g 24 LYS cc_start: 0.8984 (ptmt) cc_final: 0.8573 (ptmt) REVERT: g 49 GLU cc_start: 0.7405 (tt0) cc_final: 0.6974 (tt0) REVERT: h 34 TYR cc_start: 0.8306 (m-80) cc_final: 0.8044 (m-80) REVERT: h 40 LYS cc_start: 0.8861 (mtmt) cc_final: 0.8624 (mtpp) REVERT: h 69 ASP cc_start: 0.7822 (t0) cc_final: 0.7500 (t0) REVERT: h 99 ASP cc_start: 0.7900 (t0) cc_final: 0.7563 (t0) REVERT: i 77 GLU cc_start: 0.7797 (pt0) cc_final: 0.7597 (pt0) REVERT: i 102 SER cc_start: 0.9112 (m) cc_final: 0.8746 (p) REVERT: k 10 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7433 (ttt180) REVERT: l 68 MET cc_start: 0.8712 (mtp) cc_final: 0.8503 (mtm) REVERT: l 86 LYS cc_start: 0.9025 (tppt) cc_final: 0.8604 (tppt) REVERT: l 89 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7758 (mt-10) REVERT: n 41 MET cc_start: 0.7808 (tpt) cc_final: 0.7603 (tpp) REVERT: n 68 SER cc_start: 0.8950 (p) cc_final: 0.8557 (t) REVERT: n 85 LEU cc_start: 0.9188 (mt) cc_final: 0.8790 (mt) REVERT: n 99 ASP cc_start: 0.7970 (t0) cc_final: 0.7752 (t0) REVERT: n 119 SER cc_start: 0.9390 (t) cc_final: 0.9060 (p) REVERT: o 10 ARG cc_start: 0.8714 (mtt-85) cc_final: 0.8320 (mtt90) outliers start: 84 outliers final: 49 residues processed: 1153 average time/residue: 0.1981 time to fit residues: 363.7833 Evaluate side-chains 999 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 949 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain M residue 22 ASP Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 60 LEU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 87 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 26 ILE Chi-restraints excluded: chain m residue 37 ASN Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 88 SER Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 80 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 133 optimal weight: 40.0000 chunk 265 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 317 optimal weight: 7.9990 chunk 346 optimal weight: 0.0040 chunk 339 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 305 optimal weight: 9.9990 chunk 156 optimal weight: 2.9990 chunk 141 optimal weight: 8.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 21 GLN G 61 ASN I 76 ASN ** M 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 37 GLN P 14 HIS P 29 GLN S 32 GLN V 92 ASN W 114 HIS W 124 ASN Z 21 GLN Z 97 ASN a 55 ASN a 76 ASN c 114 HIS m 76 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.076584 restraints weight = 61365.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.079077 restraints weight = 30101.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080728 restraints weight = 18231.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.081825 restraints weight = 12731.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082571 restraints weight = 9891.182| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 32009 Z= 0.295 Angle : 0.687 7.401 43264 Z= 0.379 Chirality : 0.046 0.199 4702 Planarity : 0.004 0.046 5530 Dihedral : 10.751 78.849 4537 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.38 % Allowed : 17.61 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.14), residues: 3699 helix: 0.82 (0.16), residues: 1059 sheet: 0.01 (0.15), residues: 1086 loop : -0.24 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 47 TYR 0.023 0.002 TYR b 94 PHE 0.026 0.002 PHE i 72 TRP 0.013 0.002 TRP P 96 HIS 0.011 0.002 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.29 (32009) covalent geometry : angle 0.68737 / 0.38 (43264) hydrogen bonds : bond 0.05128 / 3.31 ( 1146) hydrogen bonds : angle 5.02487 / 3.51 ( 3192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 950 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7877 (OUTLIER) cc_final: 0.7485 (p) REVERT: B 21 GLN cc_start: 0.8165 (mt0) cc_final: 0.7876 (mt0) REVERT: B 25 ILE cc_start: 0.9189 (mt) cc_final: 0.8752 (mp) REVERT: B 63 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8558 (tt) REVERT: C 52 ASP cc_start: 0.8723 (m-30) cc_final: 0.8519 (m-30) REVERT: C 56 ASP cc_start: 0.8047 (t0) cc_final: 0.7765 (t0) REVERT: C 58 SER cc_start: 0.9131 (t) cc_final: 0.8821 (m) REVERT: C 86 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7558 (mtp-110) REVERT: D 5 LEU cc_start: 0.9270 (tp) cc_final: 0.8969 (tt) REVERT: D 12 TYR cc_start: 0.9227 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: D 94 TYR cc_start: 0.8800 (m-80) cc_final: 0.8540 (m-80) REVERT: D 97 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7081 (mm-30) REVERT: E 116 LYS cc_start: 0.8494 (tttt) cc_final: 0.8280 (ttpt) REVERT: H 77 SER cc_start: 0.9294 (t) cc_final: 0.8863 (m) REVERT: H 95 TYR cc_start: 0.8059 (t80) cc_final: 0.7472 (t80) REVERT: I 32 ASP cc_start: 0.8387 (m-30) cc_final: 0.8114 (m-30) REVERT: J 1 MET cc_start: 0.7684 (mtm) cc_final: 0.7418 (mtm) REVERT: J 12 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: J 24 SER cc_start: 0.8848 (OUTLIER) cc_final: 0.8388 (m) REVERT: K 94 ARG cc_start: 0.8884 (mtp85) cc_final: 0.8634 (mtp85) REVERT: M 18 LYS cc_start: 0.8754 (tptt) cc_final: 0.8514 (mmtt) REVERT: M 21 ILE cc_start: 0.9246 (mm) cc_final: 0.8981 (mm) REVERT: M 29 GLN cc_start: 0.8708 (mt0) cc_final: 0.8253 (mp10) REVERT: O 14 VAL cc_start: 0.8262 (t) cc_final: 0.8049 (m) REVERT: P 16 MET cc_start: 0.6439 (mmt) cc_final: 0.6058 (mmt) REVERT: P 45 GLU cc_start: 0.8147 (tt0) cc_final: 0.7515 (tt0) REVERT: P 81 PHE cc_start: 0.7825 (m-10) cc_final: 0.7107 (m-10) REVERT: S 77 SER cc_start: 0.9121 (m) cc_final: 0.8849 (p) REVERT: S 86 LYS cc_start: 0.9240 (mmtp) cc_final: 0.8993 (mmmm) REVERT: T 9 LYS cc_start: 0.8513 (mtpt) cc_final: 0.8275 (ttpp) REVERT: T 77 SER cc_start: 0.8976 (m) cc_final: 0.8464 (t) REVERT: T 94 ASN cc_start: 0.8730 (t0) cc_final: 0.8265 (t0) REVERT: U 1 MET cc_start: 0.7408 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: U 8 ILE cc_start: 0.9199 (mt) cc_final: 0.8755 (tt) REVERT: U 13 GLN cc_start: 0.8203 (tt0) cc_final: 0.7991 (mt0) REVERT: V 79 LYS cc_start: 0.8869 (tptp) cc_final: 0.8335 (ttpp) REVERT: X 168 ASP cc_start: 0.8030 (t0) cc_final: 0.7816 (t0) REVERT: Y 41 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7979 (m) REVERT: Z 94 ASN cc_start: 0.8312 (t0) cc_final: 0.8039 (t0) REVERT: a 56 ASP cc_start: 0.8771 (t0) cc_final: 0.8347 (t0) REVERT: a 58 SER cc_start: 0.8716 (t) cc_final: 0.8516 (m) REVERT: b 12 TYR cc_start: 0.9199 (OUTLIER) cc_final: 0.8345 (m-10) REVERT: b 59 ASN cc_start: 0.7974 (m-40) cc_final: 0.7759 (m-40) REVERT: c 129 TYR cc_start: 0.9145 (p90) cc_final: 0.8429 (p90) REVERT: f 50 TYR cc_start: 0.9090 (p90) cc_final: 0.8831 (p90) REVERT: f 93 ASP cc_start: 0.8096 (t0) cc_final: 0.7825 (t0) REVERT: g 49 GLU cc_start: 0.7321 (tt0) cc_final: 0.7084 (tt0) REVERT: h 31 GLU cc_start: 0.7813 (tp30) cc_final: 0.7475 (tp30) REVERT: h 69 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7572 (t0) REVERT: h 90 LYS cc_start: 0.9177 (tppt) cc_final: 0.8966 (tppt) REVERT: k 43 GLN cc_start: 0.8222 (tp-100) cc_final: 0.7844 (tp-100) REVERT: k 44 ILE cc_start: 0.9246 (mt) cc_final: 0.8650 (mt) REVERT: k 51 MET cc_start: 0.8975 (mtt) cc_final: 0.8537 (mtt) REVERT: l 68 MET cc_start: 0.8861 (mtp) cc_final: 0.8636 (mtp) REVERT: l 78 ASN cc_start: 0.8705 (m-40) cc_final: 0.8364 (m110) REVERT: l 86 LYS cc_start: 0.9068 (tppt) cc_final: 0.8807 (tppt) REVERT: m 1 MET cc_start: 0.8417 (mmm) cc_final: 0.8098 (tpt) REVERT: n 69 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7626 (t0) REVERT: n 85 LEU cc_start: 0.9311 (mt) cc_final: 0.9019 (mt) REVERT: n 119 SER cc_start: 0.9384 (t) cc_final: 0.9131 (p) REVERT: o 10 ARG cc_start: 0.8896 (mtt-85) cc_final: 0.8579 (mtt90) outliers start: 148 outliers final: 92 residues processed: 1018 average time/residue: 0.1887 time to fit residues: 308.9827 Evaluate side-chains 994 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 892 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 85 LEU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 43 GLN Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 66 ILE Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain S residue 26 ILE Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 63 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain W residue 12 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 41 VAL Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 48 LEU Chi-restraints excluded: chain a residue 71 SER Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 61 VAL Chi-restraints excluded: chain b residue 82 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain i residue 51 ASN Chi-restraints excluded: chain i residue 59 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 11 ILE Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain m residue 65 SER Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 69 ASP Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 55 SER Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 261 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 197 optimal weight: 0.9990 chunk 142 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 45 ASN E 51 ASN I 76 ASN P 14 HIS P 29 GLN W 124 ASN Z 97 ASN a 76 ASN l 21 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.078350 restraints weight = 60393.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080867 restraints weight = 29464.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082523 restraints weight = 17804.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083628 restraints weight = 12439.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.084376 restraints weight = 9658.032| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 32009 Z= 0.162 Angle : 0.593 7.892 43264 Z= 0.328 Chirality : 0.043 0.153 4702 Planarity : 0.004 0.053 5530 Dihedral : 10.596 81.885 4537 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.08 % Allowed : 19.92 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.14), residues: 3699 helix: 1.03 (0.16), residues: 1060 sheet: -0.04 (0.15), residues: 1098 loop : -0.32 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 94 TYR 0.030 0.002 TYR i 32 PHE 0.015 0.002 PHE i 72 TRP 0.024 0.002 TRP P 52 HIS 0.007 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (32009) covalent geometry : angle 0.59343 / 0.33 (43264) hydrogen bonds : bond 0.04354 / 2.83 ( 1146) hydrogen bonds : angle 4.80442 / 3.36 ( 3192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1126 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 988 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7937 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 25 ILE cc_start: 0.9120 (mt) cc_final: 0.8765 (mp) REVERT: C 58 SER cc_start: 0.9047 (t) cc_final: 0.8742 (m) REVERT: C 86 ARG cc_start: 0.7904 (ttm170) cc_final: 0.7477 (mtp-110) REVERT: D 12 TYR cc_start: 0.9130 (OUTLIER) cc_final: 0.8649 (m-80) REVERT: D 94 TYR cc_start: 0.8753 (m-80) cc_final: 0.8455 (m-80) REVERT: D 97 GLU cc_start: 0.7479 (mm-30) cc_final: 0.7113 (mm-30) REVERT: H 77 SER cc_start: 0.9278 (t) cc_final: 0.8772 (m) REVERT: H 95 TYR cc_start: 0.8019 (t80) cc_final: 0.7407 (t80) REVERT: I 32 ASP cc_start: 0.8333 (m-30) cc_final: 0.8069 (m-30) REVERT: I 86 ARG cc_start: 0.8610 (mtp85) cc_final: 0.8344 (mtt-85) REVERT: J 12 TYR cc_start: 0.8983 (OUTLIER) cc_final: 0.8114 (m-80) REVERT: J 24 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8477 (m) REVERT: J 40 LYS cc_start: 0.8854 (mtpp) cc_final: 0.8612 (mtmm) REVERT: K 9 ASP cc_start: 0.7344 (m-30) cc_final: 0.7081 (m-30) REVERT: K 94 ARG cc_start: 0.8893 (mtp85) cc_final: 0.8494 (mtt90) REVERT: M 19 ARG cc_start: 0.8432 (mtp85) cc_final: 0.8136 (mtp85) REVERT: M 21 ILE cc_start: 0.9199 (mm) cc_final: 0.8989 (mm) REVERT: M 26 LYS cc_start: 0.8573 (tttt) cc_final: 0.8347 (ttpp) REVERT: M 29 GLN cc_start: 0.8642 (mt0) cc_final: 0.8276 (mp10) REVERT: P 16 MET cc_start: 0.6060 (mmt) cc_final: 0.5502 (mmt) REVERT: P 34 GLU cc_start: 0.8312 (tp30) cc_final: 0.8061 (tp30) REVERT: P 38 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8276 (mmm-85) REVERT: P 45 GLU cc_start: 0.7997 (tt0) cc_final: 0.7520 (tt0) REVERT: P 81 PHE cc_start: 0.7828 (m-80) cc_final: 0.7395 (m-10) REVERT: P 96 TRP cc_start: 0.8241 (t-100) cc_final: 0.7875 (t-100) REVERT: P 103 ARG cc_start: 0.7966 (ptm160) cc_final: 0.7756 (ptm160) REVERT: S 77 SER cc_start: 0.9171 (m) cc_final: 0.8932 (p) REVERT: T 77 SER cc_start: 0.8900 (m) cc_final: 0.8379 (t) REVERT: T 94 ASN cc_start: 0.8741 (t0) cc_final: 0.8303 (t0) REVERT: U 8 ILE cc_start: 0.9215 (mt) cc_final: 0.8816 (tt) REVERT: U 34 ILE cc_start: 0.8877 (mm) cc_final: 0.8488 (tt) REVERT: V 79 LYS cc_start: 0.8994 (tptp) cc_final: 0.8416 (ttpp) REVERT: X 168 ASP cc_start: 0.7991 (t0) cc_final: 0.7772 (t0) REVERT: Y 19 ASP cc_start: 0.8086 (m-30) cc_final: 0.6937 (m-30) REVERT: Z 94 ASN cc_start: 0.8295 (t0) cc_final: 0.8007 (t0) REVERT: a 56 ASP cc_start: 0.8722 (t0) cc_final: 0.8338 (t0) REVERT: a 58 SER cc_start: 0.8701 (t) cc_final: 0.8486 (m) REVERT: a 85 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8631 (t) REVERT: a 95 TYR cc_start: 0.9106 (m-80) cc_final: 0.8704 (m-10) REVERT: b 12 TYR cc_start: 0.9155 (OUTLIER) cc_final: 0.8364 (m-10) REVERT: c 129 TYR cc_start: 0.9220 (p90) cc_final: 0.8545 (p90) REVERT: f 17 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8720 (mmtt) REVERT: f 50 TYR cc_start: 0.9093 (p90) cc_final: 0.8781 (p90) REVERT: f 93 ASP cc_start: 0.7949 (t0) cc_final: 0.7724 (t0) REVERT: g 25 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7366 (mm-30) REVERT: h 69 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7491 (t0) REVERT: k 43 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7724 (tp-100) REVERT: k 44 ILE cc_start: 0.9191 (mt) cc_final: 0.8620 (mt) REVERT: k 51 MET cc_start: 0.9013 (mtt) cc_final: 0.8637 (mtt) REVERT: k 78 ASN cc_start: 0.8920 (m-40) cc_final: 0.8660 (m110) REVERT: l 78 ASN cc_start: 0.8642 (m-40) cc_final: 0.8372 (m-40) REVERT: l 86 LYS cc_start: 0.9052 (tppt) cc_final: 0.8783 (tppt) REVERT: m 91 GLU cc_start: 0.7428 (mp0) cc_final: 0.6810 (mp0) REVERT: n 13 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7334 (mt-10) REVERT: n 85 LEU cc_start: 0.9275 (mt) cc_final: 0.8981 (mt) REVERT: n 119 SER cc_start: 0.9350 (t) cc_final: 0.9125 (p) REVERT: o 66 MET cc_start: 0.8669 (mtm) cc_final: 0.8442 (mtp) outliers start: 138 outliers final: 89 residues processed: 1041 average time/residue: 0.1955 time to fit residues: 324.5941 Evaluate side-chains 1026 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 930 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 81 CYS Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain M residue 10 ILE Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 14 HIS Chi-restraints excluded: chain P residue 18 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 89 MET Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain Y residue 49 SER Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain e residue 91 ILE Chi-restraints excluded: chain f residue 2 THR Chi-restraints excluded: chain f residue 31 SER Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain m residue 47 GLN Chi-restraints excluded: chain n residue 61 VAL Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 244 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 71 optimal weight: 0.7980 chunk 310 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 313 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 13 GLN D 45 ASN E 51 ASN P 29 GLN W 124 ASN Z 97 ASN a 76 ASN c 124 ASN g 10 GLN g 37 ASN h 30 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.078832 restraints weight = 60281.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081372 restraints weight = 29342.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083030 restraints weight = 17613.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.084137 restraints weight = 12254.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.084887 restraints weight = 9512.759| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32009 Z= 0.146 Angle : 0.578 7.107 43264 Z= 0.318 Chirality : 0.043 0.286 4702 Planarity : 0.003 0.040 5530 Dihedral : 10.470 83.450 4537 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.11 % Allowed : 20.86 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.14), residues: 3699 helix: 1.16 (0.16), residues: 1060 sheet: -0.17 (0.15), residues: 1116 loop : -0.31 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 94 TYR 0.036 0.002 TYR M 4 PHE 0.017 0.001 PHE i 72 TRP 0.012 0.001 TRP P 96 HIS 0.005 0.001 HIS V 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (32009) covalent geometry : angle 0.57778 / 0.32 (43264) hydrogen bonds : bond 0.04056 / 2.64 ( 1146) hydrogen bonds : angle 4.73376 / 3.32 ( 3192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 981 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7543 (p) REVERT: B 21 GLN cc_start: 0.8279 (mt0) cc_final: 0.7824 (mt0) REVERT: B 25 ILE cc_start: 0.9113 (mt) cc_final: 0.8762 (mp) REVERT: B 63 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8320 (tt) REVERT: C 86 ARG cc_start: 0.7875 (ttm170) cc_final: 0.7508 (mtp-110) REVERT: D 12 TYR cc_start: 0.9141 (OUTLIER) cc_final: 0.8726 (m-80) REVERT: D 97 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7137 (mm-30) REVERT: G 63 ILE cc_start: 0.9397 (mt) cc_final: 0.9176 (mp) REVERT: H 19 ASP cc_start: 0.8055 (m-30) cc_final: 0.7551 (m-30) REVERT: H 50 TYR cc_start: 0.8484 (p90) cc_final: 0.8276 (p90) REVERT: H 95 TYR cc_start: 0.8006 (t80) cc_final: 0.7391 (t80) REVERT: I 32 ASP cc_start: 0.8375 (m-30) cc_final: 0.8115 (m-30) REVERT: J 12 TYR cc_start: 0.8972 (OUTLIER) cc_final: 0.8104 (m-80) REVERT: J 24 SER cc_start: 0.8866 (OUTLIER) cc_final: 0.8464 (m) REVERT: M 11 GLU cc_start: 0.7218 (pm20) cc_final: 0.6907 (pm20) REVERT: M 19 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7925 (mtp85) REVERT: M 22 ASP cc_start: 0.7910 (t0) cc_final: 0.6948 (t0) REVERT: M 26 LYS cc_start: 0.8596 (tttt) cc_final: 0.8217 (mtmm) REVERT: M 29 GLN cc_start: 0.8630 (mt0) cc_final: 0.8303 (mp10) REVERT: N 7 LYS cc_start: 0.8472 (tptp) cc_final: 0.8170 (mmmt) REVERT: N 11 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7731 (pm20) REVERT: N 20 GLN cc_start: 0.8658 (mm-40) cc_final: 0.8456 (tp40) REVERT: O 6 ILE cc_start: 0.8505 (mp) cc_final: 0.7533 (mt) REVERT: O 7 LYS cc_start: 0.8634 (mtmm) cc_final: 0.8315 (mmmt) REVERT: O 14 VAL cc_start: 0.7963 (m) cc_final: 0.7380 (t) REVERT: P 16 MET cc_start: 0.5964 (mmt) cc_final: 0.5721 (mmt) REVERT: P 34 GLU cc_start: 0.8354 (tp30) cc_final: 0.8088 (tp30) REVERT: P 38 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8370 (mmm-85) REVERT: P 45 GLU cc_start: 0.8227 (tt0) cc_final: 0.7896 (tt0) REVERT: P 81 PHE cc_start: 0.7724 (m-10) cc_final: 0.7259 (m-10) REVERT: P 96 TRP cc_start: 0.8186 (t-100) cc_final: 0.7782 (t-100) REVERT: T 77 SER cc_start: 0.8916 (m) cc_final: 0.8360 (t) REVERT: T 94 ASN cc_start: 0.8747 (t0) cc_final: 0.8312 (t0) REVERT: U 8 ILE cc_start: 0.9147 (mt) cc_final: 0.8836 (tt) REVERT: U 34 ILE cc_start: 0.8881 (mm) cc_final: 0.8509 (tt) REVERT: V 79 LYS cc_start: 0.9002 (tptp) cc_final: 0.8414 (ttpp) REVERT: X 168 ASP cc_start: 0.7859 (t0) cc_final: 0.7639 (t0) REVERT: Y 19 ASP cc_start: 0.8024 (m-30) cc_final: 0.7151 (m-30) REVERT: a 56 ASP cc_start: 0.8734 (t0) cc_final: 0.8345 (t0) REVERT: a 58 SER cc_start: 0.8732 (t) cc_final: 0.8527 (m) REVERT: a 95 TYR cc_start: 0.9019 (m-80) cc_final: 0.8461 (m-10) REVERT: b 12 TYR cc_start: 0.9149 (OUTLIER) cc_final: 0.8455 (m-10) REVERT: c 129 TYR cc_start: 0.9193 (p90) cc_final: 0.8632 (p90) REVERT: f 17 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8685 (mmtt) REVERT: f 50 TYR cc_start: 0.9109 (p90) cc_final: 0.8792 (p90) REVERT: g 25 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7178 (mm-30) REVERT: g 49 GLU cc_start: 0.7277 (tt0) cc_final: 0.7074 (tt0) REVERT: h 69 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7243 (t0) REVERT: k 43 GLN cc_start: 0.8244 (tp-100) cc_final: 0.7784 (tp-100) REVERT: k 44 ILE cc_start: 0.9108 (mt) cc_final: 0.8564 (mt) REVERT: k 51 MET cc_start: 0.8978 (mtt) cc_final: 0.8650 (mtt) REVERT: l 21 GLN cc_start: 0.8677 (mt0) cc_final: 0.8444 (tt0) REVERT: l 68 MET cc_start: 0.8580 (mtp) cc_final: 0.8339 (mtt) REVERT: l 78 ASN cc_start: 0.8600 (m-40) cc_final: 0.8307 (m-40) REVERT: l 86 LYS cc_start: 0.9043 (tppt) cc_final: 0.8803 (tppt) REVERT: m 91 GLU cc_start: 0.7609 (mp0) cc_final: 0.7031 (mp0) REVERT: n 13 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7292 (mt-10) REVERT: n 85 LEU cc_start: 0.9275 (mt) cc_final: 0.9032 (mt) REVERT: n 119 SER cc_start: 0.9340 (t) cc_final: 0.9122 (p) outliers start: 139 outliers final: 93 residues processed: 1040 average time/residue: 0.1890 time to fit residues: 316.4312 Evaluate side-chains 1017 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 917 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 27 GLU Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 124 ASN Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 124 ASN Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 99 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 281 optimal weight: 8.9990 chunk 265 optimal weight: 4.9990 chunk 299 optimal weight: 8.9990 chunk 292 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 313 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 194 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 21 GLN K 124 ASN P 14 HIS P 29 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN Z 97 ASN a 76 ASN b 105 GLN c 124 ASN ** g 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.077410 restraints weight = 60363.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.079883 restraints weight = 29492.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.081515 restraints weight = 17769.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.082589 restraints weight = 12380.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083350 restraints weight = 9643.136| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 32009 Z= 0.217 Angle : 0.603 7.236 43264 Z= 0.331 Chirality : 0.044 0.262 4702 Planarity : 0.004 0.049 5530 Dihedral : 10.457 83.951 4537 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.56 % Allowed : 20.78 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3699 helix: 1.25 (0.16), residues: 1060 sheet: -0.22 (0.15), residues: 1086 loop : -0.41 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 94 TYR 0.029 0.002 TYR i 32 PHE 0.020 0.002 PHE i 72 TRP 0.010 0.001 TRP P 96 HIS 0.009 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (32009) covalent geometry : angle 0.60283 / 0.33 (43264) hydrogen bonds : bond 0.04114 / 2.68 ( 1146) hydrogen bonds : angle 4.76312 / 3.35 ( 3192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1091 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 937 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7873 (OUTLIER) cc_final: 0.7542 (p) REVERT: B 21 GLN cc_start: 0.8305 (mt0) cc_final: 0.7906 (mt0) REVERT: B 25 ILE cc_start: 0.9138 (mt) cc_final: 0.8856 (mp) REVERT: B 63 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8365 (tt) REVERT: D 12 TYR cc_start: 0.9183 (OUTLIER) cc_final: 0.8869 (m-80) REVERT: D 97 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7251 (mm-30) REVERT: G 63 ILE cc_start: 0.9402 (mt) cc_final: 0.9183 (mp) REVERT: H 53 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8472 (ttmm) REVERT: H 95 TYR cc_start: 0.8055 (t80) cc_final: 0.7422 (t80) REVERT: I 32 ASP cc_start: 0.8392 (m-30) cc_final: 0.8110 (m-30) REVERT: J 12 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: J 24 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8573 (m) REVERT: K 9 ASP cc_start: 0.7585 (m-30) cc_final: 0.7346 (m-30) REVERT: K 90 GLU cc_start: 0.7746 (tt0) cc_final: 0.7444 (tm-30) REVERT: M 11 GLU cc_start: 0.6774 (pm20) cc_final: 0.6420 (pm20) REVERT: M 26 LYS cc_start: 0.8542 (tttt) cc_final: 0.8316 (ttpp) REVERT: M 29 GLN cc_start: 0.8670 (mt0) cc_final: 0.8327 (mp10) REVERT: N 7 LYS cc_start: 0.8459 (tptp) cc_final: 0.8157 (mmmt) REVERT: N 16 LYS cc_start: 0.8938 (mmtm) cc_final: 0.8711 (tppt) REVERT: N 20 GLN cc_start: 0.8646 (mm-40) cc_final: 0.8401 (tp40) REVERT: O 14 VAL cc_start: 0.7820 (m) cc_final: 0.7262 (t) REVERT: P 16 MET cc_start: 0.6123 (mmt) cc_final: 0.5681 (mmt) REVERT: P 17 LYS cc_start: 0.9066 (tppt) cc_final: 0.8856 (tppt) REVERT: P 34 GLU cc_start: 0.8391 (tp30) cc_final: 0.8047 (tp30) REVERT: P 38 ARG cc_start: 0.8645 (mmm-85) cc_final: 0.8409 (mmm-85) REVERT: P 45 GLU cc_start: 0.8291 (tt0) cc_final: 0.7893 (tt0) REVERT: P 61 ARG cc_start: 0.8111 (mtm-85) cc_final: 0.7560 (mtm-85) REVERT: P 96 TRP cc_start: 0.8050 (t-100) cc_final: 0.7837 (t-100) REVERT: S 21 GLN cc_start: 0.7745 (mt0) cc_final: 0.7250 (tt0) REVERT: T 9 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8519 (ttpt) REVERT: T 77 SER cc_start: 0.8881 (m) cc_final: 0.8342 (t) REVERT: T 94 ASN cc_start: 0.8758 (t0) cc_final: 0.8309 (t0) REVERT: U 8 ILE cc_start: 0.9178 (mt) cc_final: 0.8933 (tt) REVERT: U 34 ILE cc_start: 0.8865 (mm) cc_final: 0.8517 (tt) REVERT: U 49 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7504 (tm-30) REVERT: V 79 LYS cc_start: 0.9024 (tptp) cc_final: 0.8428 (ttpp) REVERT: W 26 MET cc_start: 0.8958 (tpp) cc_final: 0.8077 (ttt) REVERT: X 164 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8609 (p) REVERT: X 167 GLU cc_start: 0.7731 (mp0) cc_final: 0.7526 (mp0) REVERT: X 168 ASP cc_start: 0.7986 (t0) cc_final: 0.7782 (t0) REVERT: Y 10 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7425 (tpt90) REVERT: Y 34 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8760 (tt) REVERT: a 56 ASP cc_start: 0.8841 (t0) cc_final: 0.8496 (t0) REVERT: a 58 SER cc_start: 0.8751 (t) cc_final: 0.8528 (m) REVERT: a 85 THR cc_start: 0.9038 (OUTLIER) cc_final: 0.8725 (t) REVERT: b 12 TYR cc_start: 0.9223 (OUTLIER) cc_final: 0.8526 (m-10) REVERT: c 129 TYR cc_start: 0.9211 (p90) cc_final: 0.8531 (p90) REVERT: f 17 LYS cc_start: 0.9074 (mtpp) cc_final: 0.8710 (mmtt) REVERT: f 50 TYR cc_start: 0.9094 (p90) cc_final: 0.8797 (p90) REVERT: g 25 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7179 (mm-30) REVERT: h 69 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7335 (t0) REVERT: i 60 MET cc_start: 0.8586 (ttt) cc_final: 0.8377 (ttt) REVERT: k 43 GLN cc_start: 0.8288 (tp-100) cc_final: 0.7755 (tp-100) REVERT: k 44 ILE cc_start: 0.9061 (mt) cc_final: 0.8454 (mt) REVERT: k 51 MET cc_start: 0.9037 (mtt) cc_final: 0.8673 (mtt) REVERT: l 78 ASN cc_start: 0.8585 (m-40) cc_final: 0.8267 (m-40) REVERT: l 86 LYS cc_start: 0.9074 (tppt) cc_final: 0.8836 (tppt) REVERT: m 91 GLU cc_start: 0.7688 (mp0) cc_final: 0.7103 (mp0) REVERT: n 13 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7285 (mt-10) REVERT: n 85 LEU cc_start: 0.9296 (mt) cc_final: 0.9049 (mt) REVERT: n 119 SER cc_start: 0.9352 (t) cc_final: 0.9146 (p) outliers start: 154 outliers final: 114 residues processed: 996 average time/residue: 0.1860 time to fit residues: 298.5600 Evaluate side-chains 1026 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 900 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 24 SER Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 25 LYS Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain K residue 130 GLU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 52 ILE Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 124 ASN Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 19 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 56 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Chi-restraints excluded: chain o residue 99 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 9.9990 chunk 207 optimal weight: 9.9990 chunk 274 optimal weight: 0.9980 chunk 253 optimal weight: 0.0870 chunk 43 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 279 optimal weight: 0.8980 chunk 270 optimal weight: 5.9990 overall best weight: 2.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 90 HIS K 124 ASN P 29 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN Z 97 ASN c 124 ASN e 18 GLN g 10 GLN ** m 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.094821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.077769 restraints weight = 60503.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080248 restraints weight = 29535.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.081881 restraints weight = 17775.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.082991 restraints weight = 12402.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083742 restraints weight = 9598.428| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 32009 Z= 0.177 Angle : 0.598 11.726 43264 Z= 0.325 Chirality : 0.043 0.278 4702 Planarity : 0.004 0.057 5530 Dihedral : 10.427 86.442 4537 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.59 % Allowed : 21.72 % Favored : 73.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.14), residues: 3699 helix: 1.29 (0.16), residues: 1060 sheet: -0.31 (0.15), residues: 1134 loop : -0.42 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 86 TYR 0.029 0.002 TYR i 32 PHE 0.018 0.001 PHE i 72 TRP 0.010 0.001 TRP i 89 HIS 0.004 0.001 HIS h 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (32009) covalent geometry : angle 0.59764 / 0.32 (43264) hydrogen bonds : bond 0.03980 / 2.58 ( 1146) hydrogen bonds : angle 4.76611 / 3.35 ( 3192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1105 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 950 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7861 (p) cc_final: 0.7540 (p) REVERT: A 91 ILE cc_start: 0.9385 (mt) cc_final: 0.9098 (tt) REVERT: B 21 GLN cc_start: 0.8229 (mt0) cc_final: 0.7880 (mt0) REVERT: B 25 ILE cc_start: 0.9132 (mt) cc_final: 0.8825 (mp) REVERT: B 50 TYR cc_start: 0.8971 (p90) cc_final: 0.8564 (p90) REVERT: B 63 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8338 (tt) REVERT: C 67 SER cc_start: 0.9037 (m) cc_final: 0.8825 (p) REVERT: D 12 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8871 (m-80) REVERT: D 97 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7233 (mm-30) REVERT: E 92 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7805 (mm-30) REVERT: G 63 ILE cc_start: 0.9401 (mt) cc_final: 0.9181 (mp) REVERT: H 44 ILE cc_start: 0.9277 (mp) cc_final: 0.9010 (mt) REVERT: H 53 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8459 (ttmm) REVERT: H 95 TYR cc_start: 0.8021 (t80) cc_final: 0.7346 (t80) REVERT: I 32 ASP cc_start: 0.8402 (m-30) cc_final: 0.8129 (m-30) REVERT: J 12 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8195 (m-80) REVERT: K 90 GLU cc_start: 0.7784 (tt0) cc_final: 0.7521 (tm-30) REVERT: M 5 LYS cc_start: 0.8957 (mttt) cc_final: 0.8564 (mttm) REVERT: M 11 GLU cc_start: 0.6674 (pm20) cc_final: 0.6216 (pm20) REVERT: M 26 LYS cc_start: 0.8532 (tttt) cc_final: 0.8274 (ttpp) REVERT: M 29 GLN cc_start: 0.8676 (mt0) cc_final: 0.8396 (mp10) REVERT: N 7 LYS cc_start: 0.8459 (tptp) cc_final: 0.8232 (mmmt) REVERT: N 16 LYS cc_start: 0.8935 (mmtm) cc_final: 0.8505 (mmmt) REVERT: O 14 VAL cc_start: 0.7806 (m) cc_final: 0.7289 (t) REVERT: P 16 MET cc_start: 0.6169 (mmt) cc_final: 0.5768 (tpt) REVERT: P 38 ARG cc_start: 0.8680 (mmm-85) cc_final: 0.8463 (mmm-85) REVERT: P 45 GLU cc_start: 0.8369 (tt0) cc_final: 0.7968 (tt0) REVERT: P 61 ARG cc_start: 0.8178 (mtm-85) cc_final: 0.7634 (mtm-85) REVERT: P 81 PHE cc_start: 0.7979 (m-10) cc_final: 0.7231 (m-10) REVERT: P 96 TRP cc_start: 0.8100 (t-100) cc_final: 0.7694 (t-100) REVERT: P 99 TYR cc_start: 0.8065 (t80) cc_final: 0.7508 (t80) REVERT: T 77 SER cc_start: 0.8906 (m) cc_final: 0.8344 (t) REVERT: T 94 ASN cc_start: 0.8705 (t0) cc_final: 0.8247 (t0) REVERT: U 8 ILE cc_start: 0.9172 (mt) cc_final: 0.8952 (tt) REVERT: U 34 ILE cc_start: 0.8863 (mm) cc_final: 0.8523 (tt) REVERT: V 79 LYS cc_start: 0.9048 (tptp) cc_final: 0.8459 (ttpp) REVERT: W 26 MET cc_start: 0.8971 (tpp) cc_final: 0.8324 (ttt) REVERT: X 164 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8667 (p) REVERT: X 167 GLU cc_start: 0.7708 (mp0) cc_final: 0.7486 (mp0) REVERT: X 168 ASP cc_start: 0.7924 (t0) cc_final: 0.7718 (t0) REVERT: Y 10 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7421 (tpt90) REVERT: Y 34 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8714 (tt) REVERT: a 56 ASP cc_start: 0.8828 (t0) cc_final: 0.8488 (t0) REVERT: a 58 SER cc_start: 0.8742 (t) cc_final: 0.8514 (m) REVERT: a 85 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8555 (t) REVERT: b 12 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8632 (m-80) REVERT: c 129 TYR cc_start: 0.9203 (p90) cc_final: 0.8519 (p90) REVERT: f 17 LYS cc_start: 0.9083 (mtpp) cc_final: 0.8723 (mmtt) REVERT: f 50 TYR cc_start: 0.9053 (p90) cc_final: 0.8719 (p90) REVERT: g 25 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7102 (mm-30) REVERT: h 69 ASP cc_start: 0.7863 (t0) cc_final: 0.7350 (t0) REVERT: i 60 MET cc_start: 0.8540 (ttt) cc_final: 0.8303 (ttt) REVERT: k 43 GLN cc_start: 0.8331 (tp-100) cc_final: 0.7775 (tp-100) REVERT: k 44 ILE cc_start: 0.9063 (mt) cc_final: 0.8464 (mt) REVERT: k 51 MET cc_start: 0.9014 (mtt) cc_final: 0.8657 (mtt) REVERT: l 68 MET cc_start: 0.8706 (mtp) cc_final: 0.8388 (mtm) REVERT: l 78 ASN cc_start: 0.8600 (m-40) cc_final: 0.8264 (m-40) REVERT: l 86 LYS cc_start: 0.9064 (tppt) cc_final: 0.8850 (tppt) REVERT: m 91 GLU cc_start: 0.7702 (mp0) cc_final: 0.7131 (mp0) REVERT: n 12 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7419 (t80) REVERT: n 13 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7253 (mt-10) REVERT: n 24 SER cc_start: 0.8672 (m) cc_final: 0.8428 (m) REVERT: n 85 LEU cc_start: 0.9245 (mt) cc_final: 0.8936 (mt) REVERT: n 119 SER cc_start: 0.9341 (t) cc_final: 0.9129 (p) outliers start: 155 outliers final: 115 residues processed: 1013 average time/residue: 0.1883 time to fit residues: 309.2219 Evaluate side-chains 1036 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 910 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 15 ASP Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 124 ASN Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 19 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 254 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 154 optimal weight: 8.9990 chunk 329 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 216 optimal weight: 0.0050 chunk 271 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN K 124 ASN M 37 GLN P 14 HIS P 29 GLN S 21 GLN ** U 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN c 124 ASN l 21 GLN m 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.095108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.077989 restraints weight = 60118.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080484 restraints weight = 29533.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.082116 restraints weight = 17829.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.083232 restraints weight = 12434.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.083988 restraints weight = 9619.577| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 32009 Z= 0.171 Angle : 0.601 11.564 43264 Z= 0.327 Chirality : 0.043 0.286 4702 Planarity : 0.004 0.060 5530 Dihedral : 10.398 88.031 4537 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.59 % Allowed : 22.02 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3699 helix: 1.33 (0.16), residues: 1060 sheet: -0.33 (0.15), residues: 1134 loop : -0.46 (0.17), residues: 1505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 86 TYR 0.029 0.002 TYR i 32 PHE 0.017 0.001 PHE i 72 TRP 0.011 0.001 TRP i 89 HIS 0.009 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (32009) covalent geometry : angle 0.60122 / 0.33 (43264) hydrogen bonds : bond 0.03887 / 2.52 ( 1146) hydrogen bonds : angle 4.75184 / 3.34 ( 3192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 940 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7874 (p) cc_final: 0.7539 (p) REVERT: A 51 MET cc_start: 0.8560 (mtt) cc_final: 0.8221 (mtt) REVERT: A 91 ILE cc_start: 0.9383 (mt) cc_final: 0.9135 (tt) REVERT: B 21 GLN cc_start: 0.8233 (mt0) cc_final: 0.7895 (mt0) REVERT: B 25 ILE cc_start: 0.9118 (mt) cc_final: 0.8858 (mp) REVERT: B 63 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8336 (tt) REVERT: C 67 SER cc_start: 0.9023 (m) cc_final: 0.8795 (p) REVERT: C 86 ARG cc_start: 0.8261 (ttm110) cc_final: 0.7953 (mtp-110) REVERT: D 12 TYR cc_start: 0.9166 (OUTLIER) cc_final: 0.8871 (m-80) REVERT: D 97 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7313 (mm-30) REVERT: G 63 ILE cc_start: 0.9403 (mt) cc_final: 0.9182 (mp) REVERT: H 53 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8461 (ttmm) REVERT: H 95 TYR cc_start: 0.8021 (t80) cc_final: 0.7337 (t80) REVERT: I 32 ASP cc_start: 0.8415 (m-30) cc_final: 0.8132 (m-30) REVERT: J 12 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: J 40 LYS cc_start: 0.8866 (mtpp) cc_final: 0.8561 (mttt) REVERT: J 49 TYR cc_start: 0.8816 (t80) cc_final: 0.8593 (t80) REVERT: K 90 GLU cc_start: 0.7729 (tt0) cc_final: 0.7465 (tm-30) REVERT: L 168 ASP cc_start: 0.8511 (t0) cc_final: 0.8308 (t70) REVERT: M 5 LYS cc_start: 0.8894 (mttt) cc_final: 0.8502 (mttm) REVERT: M 11 GLU cc_start: 0.6599 (pm20) cc_final: 0.6230 (pm20) REVERT: M 26 LYS cc_start: 0.8530 (tttt) cc_final: 0.8286 (ttpp) REVERT: M 29 GLN cc_start: 0.8663 (mt0) cc_final: 0.8369 (mp10) REVERT: N 16 LYS cc_start: 0.8826 (mmtm) cc_final: 0.8518 (mmmt) REVERT: N 30 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8132 (tpt90) REVERT: O 14 VAL cc_start: 0.7653 (m) cc_final: 0.7398 (p) REVERT: P 16 MET cc_start: 0.6619 (mmt) cc_final: 0.5995 (tpt) REVERT: P 34 GLU cc_start: 0.8365 (tp30) cc_final: 0.8149 (tp30) REVERT: P 38 ARG cc_start: 0.8624 (mmm-85) cc_final: 0.8364 (mmm-85) REVERT: P 45 GLU cc_start: 0.8327 (tt0) cc_final: 0.7887 (tt0) REVERT: P 61 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7273 (mtm-85) REVERT: P 81 PHE cc_start: 0.7985 (m-10) cc_final: 0.7200 (m-10) REVERT: P 96 TRP cc_start: 0.7997 (t-100) cc_final: 0.7568 (t-100) REVERT: P 99 TYR cc_start: 0.8040 (t80) cc_final: 0.7466 (t80) REVERT: P 109 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7727 (mt-10) REVERT: T 7 VAL cc_start: 0.9498 (t) cc_final: 0.9284 (p) REVERT: T 9 LYS cc_start: 0.9226 (ttpt) cc_final: 0.8984 (tttp) REVERT: T 77 SER cc_start: 0.8884 (m) cc_final: 0.8321 (t) REVERT: T 94 ASN cc_start: 0.8714 (t0) cc_final: 0.8240 (t0) REVERT: U 8 ILE cc_start: 0.9150 (mt) cc_final: 0.8859 (tt) REVERT: U 34 ILE cc_start: 0.8870 (mm) cc_final: 0.8540 (tt) REVERT: V 79 LYS cc_start: 0.9049 (tptp) cc_final: 0.8459 (ttpp) REVERT: W 26 MET cc_start: 0.9013 (tpp) cc_final: 0.8362 (ttt) REVERT: X 164 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8700 (p) REVERT: X 167 GLU cc_start: 0.7745 (mp0) cc_final: 0.7505 (mp0) REVERT: X 168 ASP cc_start: 0.7969 (t0) cc_final: 0.7716 (t70) REVERT: Y 10 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.7412 (tpt90) REVERT: Y 34 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8705 (tt) REVERT: Z 8 LYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8907 (tttm) REVERT: a 56 ASP cc_start: 0.8838 (t0) cc_final: 0.8496 (t0) REVERT: a 58 SER cc_start: 0.8721 (t) cc_final: 0.8507 (m) REVERT: a 85 THR cc_start: 0.8943 (OUTLIER) cc_final: 0.8583 (t) REVERT: b 12 TYR cc_start: 0.9210 (OUTLIER) cc_final: 0.8629 (m-80) REVERT: c 90 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: c 128 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: c 129 TYR cc_start: 0.9193 (p90) cc_final: 0.8514 (p90) REVERT: f 17 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8722 (mmtt) REVERT: f 50 TYR cc_start: 0.9107 (p90) cc_final: 0.8767 (p90) REVERT: g 25 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7200 (mm-30) REVERT: h 69 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7346 (t0) REVERT: i 60 MET cc_start: 0.8548 (ttt) cc_final: 0.8290 (ttt) REVERT: k 43 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7778 (tp-100) REVERT: k 44 ILE cc_start: 0.9080 (mt) cc_final: 0.8517 (mt) REVERT: k 51 MET cc_start: 0.9032 (mtt) cc_final: 0.8672 (mtt) REVERT: l 68 MET cc_start: 0.8733 (mtp) cc_final: 0.8111 (mtm) REVERT: l 78 ASN cc_start: 0.8613 (m-40) cc_final: 0.8243 (m-40) REVERT: l 86 LYS cc_start: 0.9071 (tppt) cc_final: 0.8806 (tppt) REVERT: m 91 GLU cc_start: 0.7731 (mp0) cc_final: 0.7174 (mp0) REVERT: n 12 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7303 (t80) REVERT: n 13 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7226 (mt-10) REVERT: n 24 SER cc_start: 0.8673 (m) cc_final: 0.8434 (m) REVERT: n 85 LEU cc_start: 0.9229 (mt) cc_final: 0.8932 (mt) REVERT: n 119 SER cc_start: 0.9341 (t) cc_final: 0.9129 (p) outliers start: 155 outliers final: 118 residues processed: 1003 average time/residue: 0.1948 time to fit residues: 315.6363 Evaluate side-chains 1045 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 913 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 14 LYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 28 LEU Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 8 LYS Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 124 ASN Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 19 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain g residue 34 ILE Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 11 ILE Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 26 MET Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 94 optimal weight: 0.0870 chunk 187 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 270 optimal weight: 7.9990 chunk 196 optimal weight: 0.0020 chunk 78 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 321 optimal weight: 9.9990 chunk 238 optimal weight: 9.9990 chunk 360 optimal weight: 1.9990 chunk 359 optimal weight: 8.9990 overall best weight: 2.8172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN K 124 ASN M 37 GLN ** N 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 GLN W 124 ASN b 92 ASN c 124 ASN m 76 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.077730 restraints weight = 60391.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.080204 restraints weight = 29706.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.081836 restraints weight = 17950.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.082946 restraints weight = 12523.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083697 restraints weight = 9702.592| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 32009 Z= 0.181 Angle : 0.623 21.765 43264 Z= 0.335 Chirality : 0.043 0.276 4702 Planarity : 0.004 0.043 5530 Dihedral : 10.378 88.917 4537 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.50 % Allowed : 22.73 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.14), residues: 3699 helix: 1.39 (0.16), residues: 1054 sheet: -0.36 (0.15), residues: 1134 loop : -0.50 (0.16), residues: 1511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 86 TYR 0.029 0.002 TYR i 32 PHE 0.018 0.001 PHE i 72 TRP 0.010 0.001 TRP i 89 HIS 0.004 0.001 HIS h 74 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (32009) covalent geometry : angle 0.62281 / 0.33 (43264) hydrogen bonds : bond 0.03883 / 2.53 ( 1146) hydrogen bonds : angle 4.74982 / 3.34 ( 3192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1090 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 938 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7873 (p) cc_final: 0.7535 (p) REVERT: A 51 MET cc_start: 0.8484 (mtt) cc_final: 0.8266 (mtt) REVERT: A 91 ILE cc_start: 0.9382 (mt) cc_final: 0.9135 (tt) REVERT: B 21 GLN cc_start: 0.8180 (mt0) cc_final: 0.7914 (mt0) REVERT: B 25 ILE cc_start: 0.9111 (mt) cc_final: 0.8861 (mp) REVERT: B 63 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8308 (tt) REVERT: C 67 SER cc_start: 0.9096 (m) cc_final: 0.8869 (p) REVERT: C 95 TYR cc_start: 0.8928 (m-80) cc_final: 0.8599 (m-80) REVERT: C 100 ASN cc_start: 0.7742 (t0) cc_final: 0.7338 (m-40) REVERT: D 12 TYR cc_start: 0.9186 (OUTLIER) cc_final: 0.8805 (m-80) REVERT: D 97 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7313 (mm-30) REVERT: G 63 ILE cc_start: 0.9398 (mt) cc_final: 0.9193 (mp) REVERT: H 53 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8472 (ttmm) REVERT: H 95 TYR cc_start: 0.8042 (t80) cc_final: 0.7802 (t80) REVERT: I 32 ASP cc_start: 0.8423 (m-30) cc_final: 0.8155 (m-30) REVERT: J 12 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8208 (m-80) REVERT: J 40 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8573 (mttt) REVERT: J 49 TYR cc_start: 0.8820 (t80) cc_final: 0.8595 (t80) REVERT: J 108 ASP cc_start: 0.8722 (t0) cc_final: 0.8517 (t0) REVERT: K 90 GLU cc_start: 0.7728 (tt0) cc_final: 0.7466 (tm-30) REVERT: L 168 ASP cc_start: 0.8473 (t0) cc_final: 0.8270 (t70) REVERT: M 5 LYS cc_start: 0.8851 (mttt) cc_final: 0.8412 (mttm) REVERT: M 19 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8323 (mtp85) REVERT: M 26 LYS cc_start: 0.8482 (tttt) cc_final: 0.8204 (ttpp) REVERT: M 29 GLN cc_start: 0.8659 (mt0) cc_final: 0.8307 (mp10) REVERT: N 16 LYS cc_start: 0.8833 (mmtm) cc_final: 0.8517 (mmmt) REVERT: N 30 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8137 (tpt90) REVERT: O 14 VAL cc_start: 0.7389 (m) cc_final: 0.7163 (p) REVERT: P 16 MET cc_start: 0.6596 (mmt) cc_final: 0.5951 (tpt) REVERT: P 34 GLU cc_start: 0.8410 (tp30) cc_final: 0.8078 (tp30) REVERT: P 38 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: P 45 GLU cc_start: 0.8334 (tt0) cc_final: 0.7865 (tt0) REVERT: P 61 ARG cc_start: 0.8148 (mtm-85) cc_final: 0.7255 (mtm-85) REVERT: P 81 PHE cc_start: 0.7992 (m-10) cc_final: 0.7274 (m-10) REVERT: P 99 TYR cc_start: 0.8064 (t80) cc_final: 0.7507 (t80) REVERT: P 109 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7707 (mt-10) REVERT: T 9 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8895 (tttp) REVERT: T 94 ASN cc_start: 0.8712 (t0) cc_final: 0.8240 (t0) REVERT: U 8 ILE cc_start: 0.9148 (mt) cc_final: 0.8871 (tt) REVERT: U 34 ILE cc_start: 0.8879 (mm) cc_final: 0.8553 (tt) REVERT: V 12 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7659 (t80) REVERT: V 79 LYS cc_start: 0.9053 (tptp) cc_final: 0.8467 (ttpp) REVERT: W 26 MET cc_start: 0.9006 (tpp) cc_final: 0.8381 (ttt) REVERT: X 164 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8729 (p) REVERT: X 167 GLU cc_start: 0.7734 (mp0) cc_final: 0.7476 (mp0) REVERT: X 168 ASP cc_start: 0.7939 (t0) cc_final: 0.7718 (t70) REVERT: Y 10 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7378 (tpt90) REVERT: Y 34 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8713 (tt) REVERT: a 56 ASP cc_start: 0.8845 (t0) cc_final: 0.8514 (t0) REVERT: a 58 SER cc_start: 0.8725 (t) cc_final: 0.8515 (m) REVERT: a 85 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8592 (t) REVERT: b 12 TYR cc_start: 0.9211 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: c 128 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7846 (pt0) REVERT: c 129 TYR cc_start: 0.9201 (p90) cc_final: 0.8581 (p90) REVERT: f 17 LYS cc_start: 0.9066 (mtpp) cc_final: 0.8732 (mmtt) REVERT: f 50 TYR cc_start: 0.9107 (p90) cc_final: 0.8786 (p90) REVERT: g 25 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7182 (mm-30) REVERT: h 69 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7370 (t0) REVERT: i 60 MET cc_start: 0.8563 (ttt) cc_final: 0.8292 (ttt) REVERT: k 43 GLN cc_start: 0.8425 (tp-100) cc_final: 0.8028 (tp-100) REVERT: k 44 ILE cc_start: 0.9077 (mt) cc_final: 0.8512 (mt) REVERT: k 51 MET cc_start: 0.9030 (mtt) cc_final: 0.8679 (mtt) REVERT: l 21 GLN cc_start: 0.8659 (mt0) cc_final: 0.8230 (tt0) REVERT: l 68 MET cc_start: 0.8664 (mtp) cc_final: 0.8378 (mtm) REVERT: l 78 ASN cc_start: 0.8633 (m-40) cc_final: 0.8216 (m-40) REVERT: l 86 LYS cc_start: 0.9028 (tppt) cc_final: 0.8759 (tppt) REVERT: m 91 GLU cc_start: 0.7744 (mp0) cc_final: 0.7216 (mp0) REVERT: n 12 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.7333 (t80) REVERT: n 13 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7218 (mt-10) REVERT: n 24 SER cc_start: 0.8684 (m) cc_final: 0.8450 (m) REVERT: n 85 LEU cc_start: 0.9244 (mt) cc_final: 0.8975 (mt) REVERT: n 114 GLU cc_start: 0.7852 (tp30) cc_final: 0.7566 (tp30) REVERT: n 119 SER cc_start: 0.9335 (t) cc_final: 0.9133 (p) outliers start: 152 outliers final: 118 residues processed: 1004 average time/residue: 0.1816 time to fit residues: 296.0150 Evaluate side-chains 1048 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 917 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 77 SER Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain P residue 102 ILE Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain T residue 87 GLU Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain Z residue 77 SER Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 19 ASP Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 11 ILE Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 86 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 233 optimal weight: 9.9990 chunk 302 optimal weight: 8.9990 chunk 257 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 226 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN K 124 ASN M 37 GLN O 20 GLN O 29 GLN P 14 HIS ** S 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 124 ASN b 92 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.095015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.077840 restraints weight = 60289.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.080319 restraints weight = 29640.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.081943 restraints weight = 17898.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.083063 restraints weight = 12483.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.083825 restraints weight = 9665.928| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32009 Z= 0.183 Angle : 0.636 20.099 43264 Z= 0.342 Chirality : 0.043 0.271 4702 Planarity : 0.004 0.053 5530 Dihedral : 10.364 89.966 4537 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.05 % Allowed : 23.62 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.14), residues: 3699 helix: 1.33 (0.16), residues: 1053 sheet: -0.41 (0.15), residues: 1134 loop : -0.43 (0.17), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 94 TYR 0.029 0.002 TYR i 32 PHE 0.018 0.001 PHE i 72 TRP 0.010 0.001 TRP i 89 HIS 0.010 0.001 HIS P 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (32009) covalent geometry : angle 0.63589 / 0.34 (43264) hydrogen bonds : bond 0.03915 / 2.56 ( 1146) hydrogen bonds : angle 4.78292 / 3.37 ( 3192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7398 Ramachandran restraints generated. 3699 Oldfield, 0 Emsley, 3699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 933 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 THR cc_start: 0.7756 (p) cc_final: 0.7425 (p) REVERT: A 51 MET cc_start: 0.8467 (mtt) cc_final: 0.8260 (mtt) REVERT: A 91 ILE cc_start: 0.9378 (mt) cc_final: 0.9128 (tt) REVERT: B 21 GLN cc_start: 0.8181 (mt0) cc_final: 0.7938 (mt0) REVERT: B 25 ILE cc_start: 0.9116 (mt) cc_final: 0.8850 (mp) REVERT: B 50 TYR cc_start: 0.8868 (p90) cc_final: 0.8426 (p90) REVERT: B 63 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8330 (tt) REVERT: C 67 SER cc_start: 0.9142 (m) cc_final: 0.8910 (p) REVERT: C 100 ASN cc_start: 0.7770 (t0) cc_final: 0.7405 (m-40) REVERT: D 12 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8886 (m-80) REVERT: D 97 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7349 (mm-30) REVERT: G 63 ILE cc_start: 0.9417 (mt) cc_final: 0.9190 (mp) REVERT: H 53 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8458 (ttmm) REVERT: H 95 TYR cc_start: 0.8018 (t80) cc_final: 0.7375 (t80) REVERT: I 32 ASP cc_start: 0.8427 (m-30) cc_final: 0.8147 (m-30) REVERT: J 12 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: J 40 LYS cc_start: 0.8873 (mtpp) cc_final: 0.8587 (mttt) REVERT: J 49 TYR cc_start: 0.8819 (t80) cc_final: 0.8598 (t80) REVERT: J 108 ASP cc_start: 0.8779 (t0) cc_final: 0.8555 (t0) REVERT: K 90 GLU cc_start: 0.7713 (tt0) cc_final: 0.7460 (tm-30) REVERT: L 168 ASP cc_start: 0.8474 (t0) cc_final: 0.8261 (t70) REVERT: M 5 LYS cc_start: 0.8812 (mttt) cc_final: 0.8451 (mttm) REVERT: M 26 LYS cc_start: 0.8512 (tttt) cc_final: 0.8290 (ttpp) REVERT: M 29 GLN cc_start: 0.8799 (mt0) cc_final: 0.8377 (mp10) REVERT: N 16 LYS cc_start: 0.8875 (mmtm) cc_final: 0.8571 (mmmt) REVERT: N 30 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8145 (tpt90) REVERT: P 16 MET cc_start: 0.6593 (mmt) cc_final: 0.5964 (tpt) REVERT: P 34 GLU cc_start: 0.8406 (tp30) cc_final: 0.8089 (tp30) REVERT: P 38 ARG cc_start: 0.8553 (mmm-85) cc_final: 0.8242 (mmm-85) REVERT: P 45 GLU cc_start: 0.8285 (tt0) cc_final: 0.7884 (tt0) REVERT: P 61 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7258 (mtm-85) REVERT: P 81 PHE cc_start: 0.7999 (m-10) cc_final: 0.7293 (m-10) REVERT: P 99 TYR cc_start: 0.8059 (t80) cc_final: 0.7485 (t80) REVERT: P 109 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7449 (mt-10) REVERT: T 9 LYS cc_start: 0.9038 (ttpt) cc_final: 0.8590 (tttm) REVERT: T 94 ASN cc_start: 0.8717 (t0) cc_final: 0.8269 (t0) REVERT: U 8 ILE cc_start: 0.9141 (mt) cc_final: 0.8883 (tt) REVERT: U 34 ILE cc_start: 0.8879 (mm) cc_final: 0.8561 (tt) REVERT: V 12 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7662 (t80) REVERT: V 79 LYS cc_start: 0.9050 (tptp) cc_final: 0.8469 (ttpp) REVERT: W 26 MET cc_start: 0.9022 (tpp) cc_final: 0.8414 (ttt) REVERT: X 164 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8753 (p) REVERT: Y 10 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7403 (tpt90) REVERT: Y 34 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8723 (tt) REVERT: a 56 ASP cc_start: 0.8840 (t0) cc_final: 0.8539 (t0) REVERT: a 85 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8595 (t) REVERT: b 12 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8630 (m-80) REVERT: c 90 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7115 (tt0) REVERT: c 128 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7856 (pt0) REVERT: c 129 TYR cc_start: 0.9209 (p90) cc_final: 0.8537 (p90) REVERT: e 86 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8421 (tppt) REVERT: f 17 LYS cc_start: 0.9091 (mtpp) cc_final: 0.8749 (mmtt) REVERT: f 50 TYR cc_start: 0.9103 (p90) cc_final: 0.8759 (p90) REVERT: g 25 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7332 (mm-30) REVERT: g 49 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7344 (mt-10) REVERT: h 69 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7403 (t0) REVERT: k 29 CYS cc_start: 0.8702 (m) cc_final: 0.8463 (m) REVERT: k 43 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8066 (tp-100) REVERT: k 44 ILE cc_start: 0.9075 (mt) cc_final: 0.8499 (mt) REVERT: k 51 MET cc_start: 0.9034 (mtt) cc_final: 0.8666 (mtt) REVERT: l 21 GLN cc_start: 0.8676 (mt0) cc_final: 0.8256 (tt0) REVERT: l 78 ASN cc_start: 0.8624 (m-40) cc_final: 0.8254 (m-40) REVERT: l 86 LYS cc_start: 0.9020 (tppt) cc_final: 0.8779 (tppt) REVERT: m 91 GLU cc_start: 0.7757 (mp0) cc_final: 0.7253 (mp0) REVERT: n 12 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7335 (t80) REVERT: n 13 GLU cc_start: 0.7595 (mt-10) cc_final: 0.7209 (mt-10) REVERT: n 24 SER cc_start: 0.8690 (m) cc_final: 0.8463 (m) REVERT: n 85 LEU cc_start: 0.9239 (mt) cc_final: 0.8964 (mt) REVERT: n 114 GLU cc_start: 0.7898 (tp30) cc_final: 0.7638 (tp30) REVERT: n 119 SER cc_start: 0.9344 (t) cc_final: 0.9078 (p) outliers start: 137 outliers final: 113 residues processed: 991 average time/residue: 0.1852 time to fit residues: 296.4363 Evaluate side-chains 1039 residues out of total 3379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 912 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 53 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 12 TYR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain G residue 2 THR Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain H residue 53 LYS Chi-restraints excluded: chain I residue 5 ASP Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 12 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 44 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 56 VAL Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 124 ASN Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain O residue 2 THR Chi-restraints excluded: chain O residue 4 TYR Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 82 LEU Chi-restraints excluded: chain S residue 2 THR Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 LEU Chi-restraints excluded: chain S residue 35 SER Chi-restraints excluded: chain S residue 39 ILE Chi-restraints excluded: chain S residue 44 ILE Chi-restraints excluded: chain S residue 73 VAL Chi-restraints excluded: chain T residue 15 ASP Chi-restraints excluded: chain T residue 35 SER Chi-restraints excluded: chain U residue 14 VAL Chi-restraints excluded: chain U residue 41 ILE Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 74 LEU Chi-restraints excluded: chain U residue 75 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 85 THR Chi-restraints excluded: chain V residue 12 TYR Chi-restraints excluded: chain V residue 39 ILE Chi-restraints excluded: chain V residue 44 SER Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 101 THR Chi-restraints excluded: chain W residue 56 VAL Chi-restraints excluded: chain W residue 61 SER Chi-restraints excluded: chain W residue 66 MET Chi-restraints excluded: chain W residue 146 LEU Chi-restraints excluded: chain X residue 164 THR Chi-restraints excluded: chain Y residue 10 ARG Chi-restraints excluded: chain Y residue 34 LEU Chi-restraints excluded: chain Y residue 37 LEU Chi-restraints excluded: chain Y residue 53 LYS Chi-restraints excluded: chain Y residue 63 ILE Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 84 ASP Chi-restraints excluded: chain Z residue 2 THR Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 43 GLN Chi-restraints excluded: chain Z residue 92 ILE Chi-restraints excluded: chain a residue 28 LEU Chi-restraints excluded: chain a residue 30 THR Chi-restraints excluded: chain a residue 85 THR Chi-restraints excluded: chain b residue 12 TYR Chi-restraints excluded: chain b residue 39 ILE Chi-restraints excluded: chain b residue 44 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain c residue 77 GLU Chi-restraints excluded: chain c residue 90 GLU Chi-restraints excluded: chain c residue 128 GLU Chi-restraints excluded: chain e residue 11 ILE Chi-restraints excluded: chain e residue 19 ASP Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 51 MET Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 39 ILE Chi-restraints excluded: chain f residue 70 SER Chi-restraints excluded: chain f residue 71 GLU Chi-restraints excluded: chain g residue 27 THR Chi-restraints excluded: chain g residue 53 VAL Chi-restraints excluded: chain g residue 85 THR Chi-restraints excluded: chain g residue 91 GLU Chi-restraints excluded: chain h residue 12 TYR Chi-restraints excluded: chain h residue 15 LEU Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 44 SER Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 69 ASP Chi-restraints excluded: chain h residue 71 LEU Chi-restraints excluded: chain h residue 106 LEU Chi-restraints excluded: chain h residue 114 GLU Chi-restraints excluded: chain h residue 126 THR Chi-restraints excluded: chain k residue 2 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 11 ILE Chi-restraints excluded: chain k residue 34 LEU Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 82 LEU Chi-restraints excluded: chain l residue 35 SER Chi-restraints excluded: chain l residue 43 GLN Chi-restraints excluded: chain l residue 77 SER Chi-restraints excluded: chain l residue 91 ILE Chi-restraints excluded: chain m residue 58 SER Chi-restraints excluded: chain m residue 67 SER Chi-restraints excluded: chain n residue 12 TYR Chi-restraints excluded: chain n residue 67 VAL Chi-restraints excluded: chain n residue 89 VAL Chi-restraints excluded: chain o residue 57 GLU Chi-restraints excluded: chain o residue 70 ASP Chi-restraints excluded: chain o residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 283 optimal weight: 7.9990 chunk 216 optimal weight: 5.9990 chunk 358 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 282 optimal weight: 4.9990 chunk 347 optimal weight: 7.9990 chunk 352 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 59 ASN K 114 HIS K 124 ASN O 20 GLN O 29 GLN W 124 ASN b 92 ASN k 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.075995 restraints weight = 61239.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.078454 restraints weight = 29836.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.080083 restraints weight = 17951.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.081180 restraints weight = 12475.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.081922 restraints weight = 9651.427| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 32009 Z= 0.261 Angle : 0.676 19.973 43264 Z= 0.364 Chirality : 0.045 0.263 4702 Planarity : 0.004 0.081 5530 Dihedral : 10.418 89.095 4537 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.14 % Allowed : 23.59 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.24 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3699 helix: 1.29 (0.16), residues: 1054 sheet: -0.36 (0.16), residues: 1092 loop : -0.56 (0.16), residues: 1553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 94 TYR 0.034 0.002 TYR i 32 PHE 0.023 0.002 PHE i 72 TRP 0.008 0.001 TRP W 89 HIS 0.005 0.001 HIS m 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00612 / 0.26 (32009) covalent geometry : angle 0.67586 / 0.36 (43264) hydrogen bonds : bond 0.04212 / 2.75 ( 1146) hydrogen bonds : angle 4.89995 / 3.45 ( 3192) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6403.62 seconds wall clock time: 111 minutes 8.45 seconds (6668.45 seconds total)